Kamakura
Closest hiking trail from Tokyo. Coastal town in the Kanagawa Prefecture. Home of the Big Buddha, Hasedera and Enoshima beach resort. The hiking trails connect to the various temples around the hills and wooded area. Mixture of nature and cultural viewings.
Okutama
Has the 2nd largest limestone cave in the Kanto region. Fall foliage is beautiful on the mountain, take in some onsen 「Hot spring 」
Nikko
City located in Tochigi Prefecture, home of the Tokugawa Shogun Shrine. The shrine comprises the gilded Yomeimon Gate, which has been repaired and painted to its splendor.
Kyoto
Former capital of Japan, the most visited city, with much culture, history and sights.
Minoo
In the northwestern part of Osaka, the mountains are covered with fall foliage, best to go in the second half of November.
Chichibu
Known for its Chichibu Kannon Pilgrimage route, visiting 34 temples located throughout the mountainous area.
Tateyama * Japan Alps
Open from April through November 30 is the Tateyama Kurobe Alpine Route. Located in Toyama Prefecture, surrounded by spectacular nature.
Nagatoro
Located in Saitama Prefecture, known for its white-water rapids. Area has been excavated for dinosaur bones.
Shikoku
88 Shikoku Pilgrimage is a well known hikers trail.
Hakuba
Also great for snowboarding and skiing
Mt. Fuji
Not to forget this hike if you are ever to choose just one. The 3776 meter high mountain invites thousands every year. From early July to mid September , no snow on the trails. You can take many trails but the ones that are most popular are the Yoshida Trail starting from the Yamanashi side of the mountain and the Subashiri Trail on the Shizuoka side, they both meet each other at the 8th station. The terrain is steep and rocky at some points. Watch out for the altitude, thinner air as you climb higher and the body is tired. Be should to wear good footwear and the right clothing. The sunrise is a spectacular sight.
Oze National Park
150 kilometers from Tokyo. Best known for the Ozegahara Marshlands and the Ozenuma Pond. Hiking from the Hatomachitoge trailhead to the Oshimizu takes around 6-8 hours for an experienced hiker.
Yakushima Island
This is an island in Kagoshima Prefecture known for their well protected wildlife and huge cedar trees. There is the loggerhead turtle nesting ground on the beach at
Nagata Inaka-hama. The Ohko Waterfall is spectacular.
If you are a hiker, enjoy the beauty of the countryside, food and the people. You will be totally satisfied with whichever hike you may take. Take care and enjoy.