15 cities
| City | Rank | 2026 Pop. ↓ | 2020 Pop. | Annual Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| Winnebago | 1 | 1,996 | 2,001 | 0.86% | 31 | 63 | Township |
| Blackbird | 2 | 1,289 | 1,268 | 1.42% | 49 | 26 | Township |
| Pender | 3 | 1,282 | 1,285 | 1.5% | 43 | 30 | Township |
| Pender | 4 | 1,070 | 1,127 | -0.83% | 1,526 | 1 | Village |
| Winnebago | 5 | 880 | 915 | -0.68% | 2,741 | 0 | Village |
| Walthill | 6 | 701 | 703 | 0% | 1,638 | 0 | Village |
| Dawes | 7 | 300 | 299 | 1.01% | 6 | 53 | Township |
| Flournoy | 8 | 270 | 266 | 1.5% | 8 | 36 | Township |
| Perry | 9 | 228 | 230 | 0.88% | 7 | 35 | Township |
| Rosalie | 10 | 153 | 158 | -0.65% | 781 | 0 | Village |
| Anderson | 11 | 126 | 123 | 0.8% | 4 | 31 | Township |
| Thurston | 12 | 116 | 118 | 0% | 410 | 0 | Village |
| Thayer | 13 | 104 | 107 | 0% | 4 | 24 | Township |
| Bryan | 14 | 85 | 85 | 1.19% | 4 | 20 | Township |
| Merry | 15 | 64 | 66 | 0% | 2 | 32 | Township |
Winnebago is the largest city in Thurston County, with a population of 1,996.
Merry is the smallest city in Thurston County, with a population of 64.
There are 15 cities in Thurston County, Nebraska.