| Rank | City | 1990 Population |
|---|---|---|
| 1 | Sioux Falls | 101,461 |
| 2 | Rapid City | 55,162 |
| 3 | Aberdeen | 25,333 |
| 4 | Watertown | 17,798 |
| 5 | Brookings | 16,384 |
| 6 | Mitchell | 13,816 |
| 7 | Pierre | 12,921 |
| 8 | Huron | 12,755 |
| 9 | Yankton | 12,404 |
| 10 | Vermillion | 10,051 |
| 11 | Spearfish | 7,178 |
| 12 | Madison | 6,387 |
| 13 | Sturgis | 6,068 |
| 14 | Belle Fourche | 4,501 |
| 15 | Hot Springs | 4,400 |
| 16 | Milbank | 3,923 |
| 17 | Lead | 3,815 |
| 18 | Mobridge | 3,777 |
| 19 | Brandon | 3,593 |
| 20 | Winner | 3,385 |
| 21 | Canton | 2,830 |
| 22 | Redfield | 2,786 |
| 23 | Box Elder | 2,673 |
| 24 | Dell Rapids | 2,497 |
| 25 | Chamberlain | 2,390 |
| 26 | Flandreau | 2,305 |
| 27 | Sisseton | 2,208 |
| 28 | Webster | 2,079 |
| 29 | North Sioux City | 2,023 |
| 30 | Fort Pierre | 1,860 |
| 31 | Beresford | 1,850 |
| 32 | Custer | 1,798 |
| 33 | Deadwood | 1,786 |
| 34 | Lennox | 1,769 |
| 35 | Miller | 1,680 |
| 36 | Lemmon | 1,640 |
| 37 | Parkston | 1,572 |
| 38 | Gregory | 1,507 |
| 39 | Gettysburg | 1,501 |
| 40 | Wagner | 1,462 |
| 41 | Elk Point | 1,423 |
| 42 | Britton | 1,369 |
| 43 | Freeman | 1,348 |
| 44 | Volga | 1,322 |
| 45 | Salem | 1,311 |
| 46 | Platte | 1,307 |
| 47 | Clark | 1,294 |
| 48 | Hartford | 1,281 |
| 49 | Clear Lake | 1,247 |
| 50 | Tyndall | 1,201 |
| 51 | Eureka | 1,197 |
| 52 | Groton | 1,196 |
| 53 | De Smet | 1,194 |
| 54 | Martin | 1,164 |
| 55 | Howard | 1,156 |
| 56 | Wessington Springs | 1,086 |
| 57 | Philip | 1,078 |
| 58 | Parker | 995 |
| 59 | Ipswich | 986 |
| 60 | Scotland | 973 |
| 61 | Garretson | 922 |
| 62 | Arlington | 919 |
| 63 | Edgemont | 908 |
| 64 | Whitewood | 891 |
| 65 | Centerville | 881 |
| 66 | Armour | 858 |
| 67 | Lake Andes | 854 |
| 68 | Alcester | 843 |
| 69 | Springfield | 838 |
| 70 | Highmore | 835 |
| 71 | Wall | 834 |
| 72 | Marion | 831 |
| 73 | St. Francis | 815 |
| 74 | Faulkton | 809 |
| 75 | Tea | 798 |
| 76 | McLaughlin | 780 |
| 77 | Menno | 771 |
| 78 | Woonsocket | 766 |
| 79 | Onida | 763 |
| 80 | Viborg | 763 |
| 81 | Burke | 756 |
| 82 | Kimball | 743 |
| 83 | Valley Springs | 739 |
| 84 | Kadoka | 736 |
| 85 | Harrisburg | 731 |
| 86 | Mission | 730 |
| 87 | Selby | 707 |
| 88 | Hill City | 700 |
| 89 | Corsica | 689 |
| 90 | Murdo | 679 |
| 91 | Newell | 675 |
| 92 | Lake Preston | 672 |
| 93 | Baltic | 670 |
| 94 | Crooks | 667 |
| 95 | Big Stone City | 664 |
| 96 | Tripp | 664 |
| 97 | Estelline | 658 |
| 98 | Colton | 657 |
| 99 | Presho | 654 |
| 100 | Waubay | 644 |
In 1990, the largest city in South Dakota was Sioux Falls, with a population of 101,461. The second largest city is Rapid City, with a population of 55,162.
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