31 cities
| City | Rank | 2025 Pop. ↓ | 2020 Pop. | Annual Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| Winnebago | 1 | 1,979 | 2,008 | 0.87% | 31 | 63 | Township |
| Winnebago | 2 | 1,979 | 2,001 | 0.87% | 31 | 63 | Township |
| Blackbird | 3 | 1,271 | 1,272 | 1.44% | 48 | 26 | Township |
| Blackbird | 4 | 1,271 | 1,268 | 1.44% | 48 | 26 | Township |
| Pender | 5 | 1,263 | 1,292 | 1.53% | 42 | 30 | Township |
| Pender | 6 | 1,263 | 1,285 | 1.53% | 42 | 30 | Township |
| Pender | 7 | 1,079 | 1,133 | -0.92% | 1,539 | 1 | Village |
| Pender | 8 | 1,079 | 1,127 | -0.92% | 1,539 | 1 | Village |
| Winnebago | 9 | 886 | 918 | -0.67% | 2,760 | 0 | Village |
| Winnebago | 10 | 886 | 915 | -0.67% | 2,760 | 0 | Village |
| Macy | 11 | 718 | 927 | -2.71% | 450 | 2 | CDP |
| Walthill | 12 | 701 | 695 | -0.14% | 1,638 | 0 | Village |
| Walthill | 13 | 701 | 703 | -0.14% | 1,638 | 0 | Village |
| Dawes | 14 | 297 | 301 | 1.02% | 6 | 53 | Township |
| Dawes | 15 | 297 | 299 | 1.02% | 6 | 53 | Township |
| Flournoy | 16 | 266 | 267 | 1.53% | 7 | 36 | Township |
| Flournoy | 17 | 266 | 266 | 1.53% | 7 | 36 | Township |
| Perry | 18 | 226 | 230 | 0.89% | 7 | 35 | Township |
| Perry | 19 | 226 | 230 | 0.89% | 7 | 35 | Township |
| Rosalie | 20 | 154 | 159 | -0.65% | 786 | 0 | Village |
| Rosalie | 21 | 154 | 158 | -0.65% | 786 | 0 | Village |
| Anderson | 22 | 125 | 124 | 0.81% | 4 | 31 | Township |
| Anderson | 23 | 125 | 123 | 0.81% | 4 | 31 | Township |
| Thurston | 24 | 116 | 118 | -0.85% | 410 | 0 | Village |
| Thurston | 25 | 116 | 118 | -0.85% | 410 | 0 | Village |
| Thayer | 26 | 104 | 107 | 0% | 4 | 24 | Township |
| Thayer | 27 | 104 | 107 | 0% | 4 | 24 | Township |
| Bryan | 28 | 84 | 85 | 1.2% | 4 | 20 | Township |
| Bryan | 29 | 84 | 85 | 1.2% | 4 | 20 | Township |
| Merry | 30 | 64 | 66 | 0% | 2 | 32 | Township |
| Merry | 31 | 64 | 66 | 0% | 2 | 32 | Township |
Winnebago is the largest city in Thurston County, with a population of 1,979.
Merry is the smallest city in Thurston County, with a population of 64.
There are 31 cities in Thurston County, Nebraska.