Japan has 47 prefectures and each prefecture boasts its unique ice cream favours that leverage home-grown ingredients. Eating ice cream is hence a great way to know more about the local produce of the prefecture you are visiting. When you happen to visit in summer, a refreshingly cool soft serve will be a lifesaver too. I have tried to consolidate some of the ice cream flavours you should look out for in Japan.
Ice cream flavours
Hokkaido Prefecture
Hokkaido milk
Lavender & melon (cantaloupe) - at Farm Tomita in Furano, Hokkaido
Chocolate - at Shiroi Koibito Park in Sapporo
Cremia
Soft serve on melon with adzuki beans - in Furano, Hokkaido (autumn menu)
Akita Prefecture
Rose petal - at Kakunodate Spring Festival
Sendai Prefecture
Sakura - at Matsushima Bay
Ibaraki Prefecture
Sakura Mochi - at Mito Plum Blossom Festival, Kairakuen
Yamanashi Prefecture
Ramune X Vanilla - at Oshino Hakkai
Tokyo Prefecture
Warabi mochi ice cream - at Kabukiza (Ginza)
Aichi Prefecture
Gold leaf - at Nagoya Castle Spring festival
Ishikawa Prefecture
Sakura - in Kanazawa
Melon-pan ice cream sandwich - at the World's Second Best Freshly Baked Melon-Pan Ice Cream shop in Kanazawa
Soy sauce ice cream - at Yamamoto Soy Sauce Miso shop in Kanazawa
Nagano Prefecture
Wasabi - at Daio Wasabi Farm, Hotaka, Matsumoto
Apple and milk ice cream - at Enza Cafe, just outside of the entrance to Jigokudani monkey park
Osaka Prefecture
Ramune - at Osaka Aquarium
Kyoto Prefecture
Black Sesame - at the Golden Pavilion (Kinkakuji)
Kyozuan tofu ice cream - not far from Fushimi Inari in Kyoto
Kagawa Prefecture
Sola shio salt ice cream - at Naoshima island

Kumamoto Prefecture
Aso milk ice cream

Okinawa Prefecture
Shikuwasa - at Blue Seal stores
Mango - at Blue Seal stores