45 cities
| City | Rank | 2025 Pop. ↓ | 2020 Pop. | Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| O'Neill | 1 | 3,577 | 3,571 | 0.03% | 1,529 | 2.34 | City |
| Atkinson township | 2 | 1,775 | 1,741 | 0.97% | 22 | 80.80 | Township |
| Atkinson | 3 | 1,312 | 1,306 | 0.08% | 802 | 1.64 | City |
| Stuart township | 4 | 836 | 795 | 1.7% | 6 | 134.81 | Township |
| Grattan township | 5 | 835 | 834 | 0.48% | 7 | 117.39 | Township |
| Stuart | 6 | 512 | 486 | 0.99% | 375 | 1.37 | Village |
| Chambers township | 7 | 434 | 429 | 0.7% | 6 | 72.07 | Township |
| Ewing township | 8 | 417 | 414 | 0.72% | 8 | 54.25 | Township |
| Ewing | 9 | 374 | 379 | -0.27% | 762 | 0.49 | Village |
| Verdigris township | 10 | 316 | 314 | 0.64% | 6 | 53.78 | Township |
| Chambers | 11 | 285 | 287 | 0% | 280 | 1.02 | Village |
| Inman township | 12 | 263 | 262 | 0.38% | 3 | 95.46 | Township |
| Page | 13 | 166 | 166 | 0% | 680 | 0.24 | Village |
| Sheridan township | 14 | 162 | 166 | -0.61% | 2 | 80.28 | Township |
| Emmet township | 15 | 140 | 139 | 0.72% | 2 | 71.12 | Township |
| Deloit township | 16 | 105 | 105 | 0% | 2 | 54.14 | Township |
| Golden township | 17 | 101 | 102 | 0% | 2 | 53.67 | Township |
| Inman | 18 | 98 | 100 | 0% | 343 | 0.29 | Village |
| Shields township | 19 | 90 | 91 | 0% | 1 | 71.97 | Township |
| Pleasant View township | 20 | 81 | 82 | 0% | 2 | 35.83 | Township |
| Wyoming township | 21 | 79 | 77 | 1.28% | 1 | 71.75 | Township |
| Sand Creek township | 22 | 75 | 73 | 1.35% | 1 | 81.21 | Township |
| Green Valley township | 23 | 74 | 72 | 1.37% | 1 | 70.46 | Township |
| Paddock township | 24 | 71 | 69 | 1.43% | 1 | 73.93 | Township |
| Conley township | 25 | 60 | 58 | 1.69% | 1 | 72.27 | Township |
| Lake township | 26 | 59 | 57 | 1.72% | 1 | 53.88 | Township |
| Rock Falls township | 27 | 50 | 48 | 2.04% | 1 | 35.99 | Township |
| Iowa township | 28 | 49 | 47 | 2.08% | 1 | 36 | Township |
| McClure township | 29 | 49 | 47 | 2.08% | 1 | 53.97 | Township |
| Emmet | 30 | 46 | 46 | 0% | 178 | 0.26 | Village |
| Saratoga township | 31 | 45 | 43 | 2.27% | 1 | 53.50 | Township |
| Swan township | 32 | 44 | 42 | 2.33% | 0.00 | 106.66 | Township |
| Shamrock township | 33 | 42 | 40 | 2.44% | 1 | 54.41 | Township |
| Coleman township | 34 | 40 | 40 | 0% | 1 | 52.70 | Township |
| Scott township | 35 | 39 | 39 | 0% | 1 | 66.14 | Township |
| Willowdale township | 36 | 39 | 39 | 0% | 1 | 72.01 | Township |
| Belle township | 37 | 38 | 38 | 0% | 1 | 35.90 | Township |
| Cleveland township | 38 | 38 | 38 | 0% | 0.00 | 85.80 | Township |
| Fairview township | 39 | 36 | 36 | 0% | 1 | 53.71 | Township |
| Antelope township | 40 | 33 | 33 | 0% | 1 | 36.09 | Township |
| Steel Creek township | 41 | 26 | 26 | 0% | 0.00 | 65.40 | Township |
| Francis township | 42 | 24 | 24 | 0% | 0.00 | 53.78 | Township |
| Holt Creek township | 43 | 24 | 24 | 0% | 0.00 | 52.69 | Township |
| Josie township | 44 | 22 | 22 | 0% | 1 | 35.86 | Township |
| Dustin township | 45 | 19 | 19 | 0% | 0.00 | 59.84 | Township |
O'Neill is the largest city in Holt County, with a population of 3,577.
Dustin township is the smallest city in Holt County.
There are 45 cities in Holt County, Nebraska.