Japan has hundreds upon hundreds of hot springs resort areas.  Some of these onsen areas are quite famous while some may never have been heard of even by Japanese who have frequented various hot springs resort areas throughout their lives.  Below are  popular hot sprigs resort areas listed by prefecture:

Popular Hot Springs Resort Areas by Prefecture:

Aichi-Inuyama City

Aichi-Kira Onsen

Aichi-Miya Onsen
Aichi-Nishiura Onsen
Aichi Utsumi Onsen
Aichi-Yamani - Kaigan Beach
Aichi-Yuya Onsen
Akita-Oga Onsen
Akita-Yuze Onsen
Aomori-Oowani Onsen

Aomori-Towada Lake (Yasumiya)
Chiba-Awa-Kominato
Chiba-Kamogawa City
Chiba-Inubozaki Cape
Chiba-Yorokeikoku Onsen
Ehime-Dogo Onsen
Fukui-Awara Onsen
Fukui-Tojinbo Onsen
Fukuoka- Chikugogawaonen
Fukuoka-Futsukaichi Onsen
Fukuoka-Harazuru Onsen
Fukushima-Ashinomaki Onsen
Fukushima-Bandaiatami Onsen
Fukushima-Dake Onsen
Fukushima-Higashiyama Onsen
Fukushima-Iizaka Onsen
Fukushima-Iwakiyumoto Onsen
Fukushima-Omotebandai-Kogen Plateau
Fukushima-Tsuchiyu Onsen
Gifu-Enakyo, Ena City
Gifu-Gero Onsen
Gifu-Hida-Furukawa
Gifu-Hirayu Onsen
Gifu-Nagaragawa Onsen
Gifu-Shinhirayu Onsen
Gifu-Shinhotaka Onsen
Gifu-Takayama City
Gunma-Ikaho Onsen
Gunma-Kusatsu Onsen
Gunma-Minakami Onsen
Gunma-Oigami Onsen
Gunma-Shima Onsen
Gunma-Tanigawa Onsen
Hiroshima-Fukuyama City(Tomonura)
Hiroshima-Miyahama Onsen
Hokkaido-Abashiri City
Hokkaido-Akanko Onsen
Hokkaido-Iwani Onsen
Hokkaido-Jozankei Onsen, Sapporo
Hokkaido-Kawayu Onsen
Hokkaido-Mashu Onsen
Hokkaido-Niseko-Hirafu Ski Resort
Hokkaido-Noboribetsu Onsen
Hokkaido-Onneyu Onsen
Hokkaido-Onneyu Onsen
Hokkaido-Sounkyo Onsen
Hokkaido-Tenninkyo Onsen
Hokkaido-Tokachigawa Onsen
Hokkaido-Toyako Onsen
Hokkaido-Utoro Onsen, Shiretoko
Hokkaido-Yunokawa Onsen
Hyogo-Ako City (Misaki)
Hyogo-Arima Onsen, Kobe
Hyogo-Fukura, Awajishima Island
Hyogo-Kinosaki Onsen
Hyogo-Shiota Onsen

Hyogo-Sumoto Onsen, Awajishima Island

Hyogo-Takarazuka Onsen
Ibaraki-Tsukaba
Ishikawa-Awazu Onsen
Ishikawa-Katayamazu Onsen
Ishikawa-Tatsunokuchi Onsen 
Ishikawa-Wajima City
Ishikawa-Wakura Onsen
Ishikawa-Yamanaka Onsen
Ishikawa-Yamashiro Onsen
Iwate-Hanamaki Onsen 
Iwate-Ichinoseki City 
Iwate-Minami-Hanamaki Onsen Resorts 
Iwate-Tsunagi Onsen 
Kagawa-Kotohira 
Kagoshima-Ibusuki Onsen 
Kagoshima-Kagoshima City 
Kagoshima-Kirishima Onsen
Kagoshima-Myoken Onsen 
Kanagawa-Hakone (Hakone-yumoto)
Kanagawa-Yugawara Onsen
Kochi-Kochi City
Kumamoto-Amakusa (Hondo City)
Kumamoto-Aso
Kumamoto-Hitoyoshi Onsen
Kumamoto-Kikuchi Onsen
Kumamoto-Kumamoto City
Kumamoto-Kurokawa Onsen
Kumamoto-Yamaga Onsen
Kyoto-Amanohashidate, Miyazu City
Kyoto-Kitsu Onsen, Tango Peninsula
Kyoto-Kyoto City (Ukyo-ku) 
Kyoto-Miyazu City 
Kyoto-Yunohana Onsen
Mie-Futaminoura
Mie-Hamajima
Mie-Sakakibara Onsen
Mie-Toba City
Mie-Yunoyama Onsen
Miyagi-Akiu Onsen, Sendai
Miyagi-Matsushima
Miyagi-Naruko Onsen
Miyagi-Obara Onsen
Miyazaki-Aoshima, Nichinan Coast
Miyazaki-Miyazaki City
Nagano-Asama Onsen
Nagano-Bessho Onsen 
Nagano-Hakuba-Happone
Nagano-Kamikochi
Nagano-Kamisuwa Onsen 
Nagano-Matsumoto City (Tobira Onsen)Nagano-Nozawa Onsen 
Nagano-Oomachi Onsen
Nagano-Shibu Onsen
Nagano- Shiga Kogen Plateau (Hoppo)
Nagano-Shirahone Onsen 
Nagano-Togura-Kamiyamada Onsen
Nagano-Yamada Onsen
Nagano-Yudanaka Onsen 
Nagasaki-Hirado City
Nagasaki-Unzen Onsen 
Nara-Nara City
Nara-Totsukawa Onsen
Nara-Yoshinoyama 
Niigata-Akakura Onsen
Niigata-Matsunoyama Onsen