In Japan, the mundane and the sacred interact in beautiful, delicate ways. Within a block, skyscrapers and neon streets give way to antique halls where monks sing in the morning light, torii gates with trees, and mossy stone lanterns. Many visitors discover that going to shrines and temples in Japan is more about reevaluating their pace, taking a personal break, and enjoying a quiet hall and a trained bow than it is about seeing all the sights. This guide is designed for the spiritual traveler who wants more than simply pictures; who wants to meditate, experience the ritual and history, and go home with a sense of accomplishment.

Below is a detailed, practical, and thoughtful discussion of the four spiritual experiences that comprise the wonderful, multi-layered pilgrimage through Japan: the monasteries of Mount Koya (Koya-san) in Wakayama, the Ise Grand Shrine in Mie Prefecture, the Meiji Shrine in Tokyo, and Zen (zazen) practice sites across the country. I’ll go over what to expect, proper conduct (etiquette), when to go, suggested itineraries, and tips for a more thoughtful and rewarding visit.

Why pilgrimage in Japan feels different

Shinto, an indigenous religion centered on nature, and Buddhism, which was introduced to Japan centuries ago, have a significant impact on the religious landscape of the nation. Shrine (jinja), typically Shinto, honors kami, spirits associated with nature, ancestors, or founding myths. Monks, sutras, meditation, and burial rites are usually held at Buddhist temples, sometimes referred to as dera or tera. However, the lived experience in Japan blends the two; births and seasonal festivals are celebrated at Shinto shrines, while funerals are held at Buddhist temples.

Among the customs and small moments that tourists will witness everywhere are a family buying Omamori (protection charms), a bride and groom dressed traditionally, an old person quietly washing their hands at a temizuya (purification basin), or monks leading morning prayer. Approaching these places with quiet curiosity and basic politeness can open doors—sometimes literally—and provide a far more profound experience than simply viewing them from the outside.

Meiji Shrine (Meiji Jingū) : Tokyo’s calming heart

Why go: Meiji Shrine offers a concentrated experience of Shinto ritual inside Tokyo’s urban sprawl. Walkable from Harajuku and Shibuya, its broad gravel paths and dense forest make it surprisingly cool, calm, and removed from the city bustle.

A brief history: Meiji Shrine was completed in 1920 thanks to national donations and engagement. It was founded to honor the deified souls of Emperor Meiji and Empress Shoken. Even though the original buildings were destroyed during World War II and then reconstructed, the shrine is today a vibrant center for marriages, seasonal events, and everyday devotion. You can visit Meiji Shrine from dawn to dusk. Although the precinct is free to enter, some of the cultural events there may be fee-based.

What to do there

• Enter through a torii and walk the forested approach. The walk itself functions like a quieting ritual: as you pass through the torii, slow your pace and notice the change in sound and light.
• Purify at the temizuya. Use the ladles to rinse your hands and mouth (don’t drink directly). It’s a simple symbolic cleansing—use right, left, then mouth, then ladle handle.
• Observe (or participate in) a Shinto ritual. If a service is taking place at the main hall you can bow respectfully and watch. Weddings in Shinto style (shinzen kekkon) are common; if you see one, keep your distance and photograph only with permission or discretely from afar.
• Write an ema or buy an omamori. Ema wooden plaques are for wishes; write a short, simple note and hang it. Omamori (charms) are available for health, travel safety, exams, and more—perfect tangible tokens of the visit.
• Explore the Inner Garden (Meiji Jingu Gyoen) on some days—this is a serene landscape garden that carries seasonal beauty.

Etiquette & practical tips

• Silence and restraint: speak softly, avoid sudden movements, and switch your phone to silent.
• Photography: allowed in most areas, but not inside prayer halls during formal rituals.
• Timing: early morning is magical—fewer crowds and softer light. New Year’s (Hatsumode) sees huge crowds if you want an intense pilgrimage experience; otherwise avoid those peak festival days if you prefer quiet.

Good for: first-time seekers who want a quick yet profound encounter with Shinto in the heart of Tokyo.

Ise Grand Shrine (Ise Jingū) : Japan’s spiritual home

Why go: It is common to refer to Ise Jingū as the spiritual center of Japan. Its major sanctuary (Naikū) honors Amaterasu-Ōmikami, the sun goddess and ancestral kami of the imperial family. The entire complex, which is made up of over a hundred shrines connected by ritual routes and holy woodlands, is an example of a continuity of ritual and construction that is uncommon in other places. A visit to Ise should include both seeing monuments and strolling through a spiritual region.

A brief history & significance
Ise’s Naikū is believed to have been enshrining Amaterasu for roughly two thousand years; the structure and rites have been kept by shikinen sengū, a periodic restoration method that preserves the shrine’s techniques and purity. This ritual renewal emphasizes Shinto’s concern for continuity, rebirth, and the maintenance of sacred sites. Because of the myths surrounding Amaterasu and the shrine’s imperial connections, many Japanese consider Ise to be a premier pilgrimage destination.

What to expect at Naikū and Gekū

• Naikū (Inner Shrine): The most sacred site—approach quietly and respectfully. Photography is restricted in the most sacred precincts; follow signage and staff direction.
• Gekū (Outer Shrine): Also very important; historically associated with Toyouke-no-Ōkami (deity of food and industry). Both shrines are linked by the ancient pilgrimage route through the town of Uji-Yamada, which is charming and lined with specialty food shops and local crafts.
• Forest setting & rivers: The shrines sit within a large, protected forest. Parts of the approach include wooden bridges, pebbled paths, and clean running streams—elements that encourage reflection as you walk.

Practices and rituals

• Offerings and bows: At main halls you’ll see the typical Shinto practice of offering a coin in the offering box, bowing twice, clapping twice, offering a prayer, and bowing once. Observe and mirror local practice.
• Omikuji (fortune slips): Common across shrines. If your fortune reading is bad, tie it to the designated rack to leave the bad luck behind.
• Respect the inner sanctum: Some spaces are closed to the public; honor those boundaries.

Access & visitor logistics
Ise may be reached by train from Nagoya (direct services are also available via the Kintetsu Railway). Many tourists establish themselves in Ise City (Uji-Yamada), where accommodations range from modern hotels to ryokan. Give yourself at least a full day to explore Naikū and Gekū, including time to meander through the nearby holy forests and shopping avenues.

Good for: travelers wanting a deep, historically anchored Shinto experience—this is the place to slow down, walk, and feel Japan’s ancestral reverence.

Mount Kōya (Koya-san) :  monastic life and overnight temple stays

Why go: Koya-san is one of Japan’s most fascinating religious centers. Founded by the monk Kūkai (Kōbō Daishi) in the ninth century, it features a full hilltop settlement with temples and lantern-lit walkways, as well as the vast and haunting Okunoin cemetery. Staying in a shukubō (temple guesthouse) and going to morning services is one way to experience esoteric Shingon Buddhism.

What makes Koya-san special

• Okunoin cemetery: One of Japan’s largest and most mystical cemetery complexes, where towering cedar trees overshadow stone memorials and lanterns leading toward Kōbō Daishi’s mausoleum. Many Japanese pilgrimage here to pay respects, and the atmosphere at dusk or dawn is profound.
• Temple lodgings (shukubō): Over fifty temples welcome guests. A stay often includes tatami rooms, vegetarian shojin ryori meals, participation in chanting or morning service, and sometimes guided meditation or sutra copying. It’s minimalistic and intentionally contemplative.
• Monastic rituals: Fire ceremonies, morning chanting, and ritualized incense offerings provide a window into living Buddhist practice. Many visitors find the schedule of a temple stay—early rising, chants, simple meals—instantly clarifying and rejuvenating.

How to plan a stay

• Book a shukubō in advance, especially in busy seasons. Temple websites and reputable booking platforms list availability and what activities are included.
• Expect simple comforts: futon bedding, shared bathrooms in many places (though private baths can be available), and no Wi-Fi in some more traditional lodgings—an intentional unplug.
• Try Ajikan and seated meditation: Many temples offer meditation practice suited to beginners; the Ajikan (visualization of the letter A) is a distinctive practice of Shingon and often taught to visitors.

Etiquette

• Follow the temple’s schedule and instructions; it’s a living place, not just tourist accommodation.
• Dress modestly for ceremonies and remove shoes at thresholds.
• Be on time for morning and evening events; punctuality is part of the respect shown to monks and fellow guests.

Good for: travelers craving a real monastic experience—less sightseeing and more sustained stillness.

Zen meditation (Zazen) — sitting with the breath

Why go: Because of Zen’s approachable focus on posture, breath, and present, zazen is an excellent way for travelers to start meditation. Whether you attend a one-day session near Tokyo or a multi-day sesshin (intense retreat) in Kyoto or rural temples, zazen makes concentration easier and often results in immediate calm.

What is zazen?
Zazen is seated meditation in its most basic form, with an emphasis on breathing, posture, and nonjudgmental awareness. A session may begin with a brief teaching by a monk or master, followed by periods of peaceful sitting and sometimes kinhin (walking meditation). In more advanced practice, Zen uses koans, or paradoxical questions, to combat mental tendencies, even though the majority of visiting sessions focus on posture and breath.

Where to practice

• Urban temples: In Kyoto and Tokyo many temples offer one-hour introductory zazen sessions for foreigners, suitable for first-timers.
• Monastic stays: At Koya-san or other temple lodgings you can often join morning zazen as part of the daily schedule.
• Dedicated centers: Zen centers aimed at international visitors run English-friendly lessons and retreats. Check temple websites or tourist resources for reservation details. Japan Travel+1

What to wear and what to expect

• Comfortable, modest clothing that allows sitting cross-legged or on a zafu (meditation cushion) is ideal. Long skirts and tight clothing can be uncomfortable.
• Posture guidance: instructors will show the full lotus, half lotus, or the Burmese posture, and alternatives for those with knee/back issues.
• Time commitment: a typical introductory session is 45–90 minutes; multi-day retreats vary from 2-3 days to a full week.
• Language: many temples offer instruction in English or provide English handouts; larger centers in Kyoto and Tokyo tend to be most user-friendly for non-Japanese speakers.

A few practical meditation tips

• Let go of expectations. Zazen is less about achieving a specific state and more about returning attention to the present moment.
• Start with small steps. A short, regular practice is more beneficial than a single long session.
• Use breath as an anchor. Focus on the sensations of breathing at the belly rather than trying to control it.

Good for: travelers wanting to learn a practical technique for calm and presence that can be used anywhere.

Sample spiritual itineraries

Below are two itineraries that weave the four experiences into coherent trips. You can adapt them by pace and interests.

6-day “Essentials” (Tokyo → Koya-san → Kyoto)

• Day 1: Arrive Tokyo. Gentle wandering in Harajuku; evening stroll to Meiji Shrine for sunset light and an introductory Shinto experience.
• Day 2: Morning at Meiji Shrine, purification, ema, stroll through the Inner Garden. Afternoon travel (bullet train + local) toward Kansai or overnight train/flight to Osaka.
• Day 3: Transfer to Koya-san. Afternoon exploration and evening temple lodging; participate in evening service.
• Day 4: Early morning service/meditation; walk Okunoin; afternoon transfer to Kyoto.
• Day 5: Join a Zen zazen session at a Kyoto temple; visit Kiyomizu-dera or other quieter temples in the afternoon.
• Day 6: Optional day trip to Ise (if you rearrange travel) or depart from Kansai Airport.

9–11 day “Deep Pilgrimage” (Tokyo → Ise → Koya-san → Kyoto)

• Days 1–2: Tokyo & Meiji Shrine (slow start, acclimate).
• Days 3–4: Travel to Ise City. Spend full day at Naikū and Gekū, explore Uji-Yamada, attend seasonal rituals if available.
• Days 5–6: Travel west toward Koya-san; settle into a shukubō, participate in rituals and meditate.
• Days 7–9: Kyoto: zazen sessions, temple visits, time for reflective walking in Arashiyama or the Philosopher’s Path.
• Day 10–11: Buffer days for travel delays and quiet departure.

Practicalities, packing list, and etiquette quick reference

Packing (spiritual travel essentials):

• Comfortable layers for early mornings and cool forest shade.
• Modest clothing for temple/shrine visits (shoulders covered; avoid short shorts).
• Slip-on shoes (many places require removing shoes).
• Small towel or handkerchief for purity rites and sweat on warm days.
• Notebook & pen for reflections or copying sutras (if you try it).
• Reusable water bottle (refillable at conbini or hotel).

Etiquette quick tips

• Bow at torii gates (a small bow as a sign of respect) and when entering worship halls.
• Keep voice low and mobile phones silent.
• No shoes in temple buildings, follow the lead of locals and staff.
• Offerings: if you toss a coin, avoid large bills; 5 yen coins are often used because the Japanese word for five yen (go-en) is a homophone for “good fate” or “good relationship.”
• Photography: look for signs, no-photo zones are common in inner sanctums or during rituals.
• Follow the lead of shrine/temple staff during ceremonies; many places are very welcoming to respectful visitors.

A few reflective practices to try while visiting

1. Walking meditation between torii gates. Use the path as your guide: breathe in, count steps quietly to ten, then reverse the count, repeat. Let traffic and noise fade into the background.
2. Ema reflection. Before writing an ema, sit quietly for two minutes and condense one meaningful wish or intention. Keep it short and sincere.
3. Morning service participation. If staying at a shukubō, wake for morning chants, even five minutes of listening helps reframe the rest of the day.
4. Sutra copying (shakyo). Many temples offer the chance to copy sutras slowly with a brush; it’s a slow, meditative act that cultivates focus.
5. Silent sitting in a temple garden. Find a bench or step in a garden and set a five-minute timer. Watch thoughts come and go without chasing them.

Safety, accessibility, and respectful engagement

• Accessibility: major sites like Meiji Shrine provide accessibility information (wheelchairs available at entrances). If you or your travel companions have mobility needs, check shrine pages or contact visitor offices in advance.
• Weather: forested and coastal shrines can be damp bring waterproof layers in rainy seasons. Summers are hot and humid; temples with shaded gardens offer respite.
• Language: while many temples welcome foreigners, English may not be spoken widely in smaller shrines—carry a translation app or a few polite phrases in Japanese. Most major pilgrimage sites provide English signage or handouts.

Pilgrimage = presence

A stance of respectful curiosity and calm concentration is rewarded in spiritual travel in Japan. Whether you decide to spend the night in the quiet halls of Koya-san, walk the ancient paths of Ise to feel the mythic undercurrent of the country, visit Meiji Shrine for a city-centered renewal, or sit in silence during a zazen session, every visit is an invitation to slow down, pay attention, and return home a little more peaceful.

In this context, pilgrimage is not a checklist but rather a collection of small rituals that, when taken together, create a lived sense of hallowed time. For many travelers, the most memorable part of a trip is that silent accumulation of moments—one deep bow, one focused breath, one dawn chant.