populations of the next three largest cities: Yokohama, Osaka, and Nagoya.
Cities with populations exceeding 100,000 are ranked below in two columns:
| Population | City | Population | City |
| 8,163,573 | Tokyo | 194,947 | Ageo |
| 3,220,331 | Yokohama | 194,866 | Yamato |
| 2,623,801 | Osaka | 193,417 | Odawara |
| 2,154,793 | Nagoya | 188,823 | Kasukabe |
| 1,671,742 | Sapporo | 188,563 | Kishiwada |
| 1,477,410 | Kobe | 186,134 | Itami |
| 1,461,103 | Kyoto | 185,938 | Nagaoka |
| 1,237,062 | Fukuoka | 177,010 | Uji |
| 1,173,603 | Kawasaki | 175,466 | Takaoka |
| 1,085,705 | Hiroshima | 175,053 | Ube |
| 1,026,455 | Kitakyushu | 174,704 | Hirosaki |
| 918,398 | Sendai | 174,307 | Kamakura |
| 829,455 | Chiba | 174,105 | Suzuka |
| 807,765 | Sakai | 169,963 | Saga |
| 593,730 | Okayama | 167,686 | Ashikaga |
| 579,306 | Kumamoto | 167,384 | Obihiro |
| 536,752 | Kagoshima | 165,928 | Hino |
| 534,620 | Hamamatsu | 165,564 | Mitaka |
| 533,270 | Funabashi | 164,013 | Kodaira |
| 531,542 | Sagamihara | 163,211 | Otaru |
| 518,319 | Higashi-Osaka | 160,118 | Tomakomai |
| 498,999 | Amagasaki | 157,372 | Moriguchi |
| 486,097 | Niigata | 157,309 | Sayama |
| 472,196 | Shizuoka | 157,177 | Tsu |
| 466,347 | Hachioji | 155,620 | Hadano |
| 456,210 | Matsudo | 152,824 | Tachikawa |
| 454,360 | Himeji | 152,124 | Kumagaya |
| 444,599 | Nagasaki | 151,471 | Narashino |
| 443,322 | Matsuyama | 150,453 | Omuta |
| 442,868 | Kanazawa | 148,615 | Yachiyo |
| 438,680 | Kawaguchi | 148,281 | Ogaki |
| 436,596 | Ichikawa | 146,127 | Izumi (Miyagi) |
| 433,358 | Yokosuka | 144,688 | Sakura |
| 426,909 | Nishinomiya | 144,489 | Tama |
| 426,795 | Utsunomiya | 143,396 | Tsuruoka |
| 418,271 | Urawa | 142,956 | Matsue |
| 414,693 | Kurashiki | 142,467 | Tottori |
| 410,324 | Gifu | 142,297 | Kadoma |
| 409,837 | Toyonaka | 142,262 | Oyama |
| 408,501 | Oita | 142,251 | Anjo |
| 403,776 | Omiya | 141,253 | Kawanishi |
| 396,553 | Wakayama | 140,059 | Nagareyama |
| 390,788 | Hirakata | 139,801 | Ota |
| 365,612 | Fukuyama | 139,077 | Musashino |
| 359,867 | Takatsuki | 138,919 | Niiza |
| 359,071 | Asahikawa | 137,585 | Imari |
| 355,812 | Iwaki | 135,919 | Matsubara |
| 350,330 | Fujisawa | 134,002 | Higashi-Murayama |
| 349,349 | Nara | 131,453 | Yonago |
| 349,050 | Machida | 130,624 | Nobeoka |
| 347,026 | Nagano | 130,334 | Beppu |
| 345,206 | Suita | 130,153 | Miyakonojo |
| 337,982 | Toyohashi | 130,116 | Joetsu |
| 332,336 | Toyota | 129,680 | Kakamigahara |
| 329,684 | Takamatsu | 129,461 | Yamaguchi |
| 321,254 | Toyama | 129,149 | Niihama |
| 317,069 | Kochi | 128,376 | Misato |
| 314,642 | Koriyama | 127,471 | Tsuchiura |
| 307,249 | Hakodate | 126,460 | Daito |
| 306,822 | Okazaki | 126,446 | Kiryu |
| 305,058 | Kashiwa | 126,340 | Seto |
| 304,854 | Kawagoe | 125,960 | Ome |
| 304,836 | Naha | 124,441 | Komaki |
| 303,040 | Tokorozawa | 123,433 | Kisarazu |
| 302,362 | Akita | 123,114 | Imabari |
| 287,808 | Aomori | 122,120 | Minoo |
| 287,352 | Miyazaki | 121,976 | Ishinomaki |
| 286,261 | Maebashi | 120,628 | Abiko |
| 285,259 | Koshigaya | 120,126 | Kariya |
| 277,568 | Yao | 119,815 | Fujieda |
| 277,528 | Fukushima | 119,435 | Ueda |
| 274,180 | Yokkaichi | 119,080 | Aizu-Wakamatsu |
| 270,722 | Akashi | 118,725 | Matsusaka |
| 266,599 | Kasugai | 117,855 | Muroran |
| 263,356 | Tokushima | 117,634 | Hofu |
| 262,635 | Shimonoseki | 117,092 | Fujinomiya |
| 262,434 | Ichinomiya | 115,938 | Isezaki |
| 260,018 | Otsu | 115,675 | Urayasu |
| 257,716 | Ichihara | 115,554 | Kashihara |
| 256,524 | Neyagawa | 115,049 | Habikino |
| 254,078 | Ibaraki | 114,475 | Noda |
| 252,743 | Fukui | 113,818 | Higashi-Kurume |
| 249,487 | Yamagata | 112,186 | Yaizu |
| 245,950 | Hiratsuka | 112,102 | Zama |
| 244,677 | Sasebo | 111,730 | Toyokawa |
| 241,523 | Shimizu | 110,900 | Tokuyama |
| 241,057 | Hachinohe | 110,447 | Tondabayashi |
| 239,803 | Kakogawa | 109,825 | Katsuta |
| 236,461 | Takasaki | 109,530 | Iwakuni |
| 235,434 | Morioka | 108,767 | Kawachi-Nagano |
| 234,968 | Mito | 108,135 | Yatsushiro |
| 228,347 | Kurume | 107,247 | Kitami |
| 222,490 | Fuji | 106,462 | Iwatsuki |
| 216,723 | Kure | 106,075 | Komatsu |
| 211,732 | Numazu | 105,899 | Koganei |
| 209,396 | Fuchu | 105,882 | Ebina |
| 206,132 | Soka | 105,845 | Okinawa |
| 205,639 | Kushiro | 105,418 | Mishima |
| 202,141 | Hitachi | 105,372 | Akishima |
| 201,862 | Takarazuka | 104,218 | Ikeda |
| 201,675 | Chigasaki | 104,164 | Ise |
| 200,715 | Matsumoto | 103,617 | Asaka |
| 200,626 | Kofu | 100,982 | Kokubunji |
| 197,677 | Chofu | 100,811 | Sakata |
| 197,283 | Atsugi |
