16 cities
| City | Rank | 2025 Pop. ↓ | 2020 Pop. | Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| Winnebago township | 1 | 1,946 | 2,004 | 0% | 31 | 63.41 | Township |
| Blackbird township | 2 | 1,234 | 1,268 | 0% | 47 | 26.27 | Township |
| Pender township | 3 | 1,213 | 1,282 | -0.33% | 41 | 29.94 | Township |
| Pender | 4 | 1,015 | 1,110 | -1.84% | 1,448 | 0.70 | Village |
| Winnebago | 5 | 868 | 918 | -1.14% | 2,704 | 0.32 | Village |
| Macy | 6 | 718 | 927 | -2.71% | 450 | 1.59 | CDP |
| Walthill | 7 | 675 | 692 | -0.44% | 1,577 | 0.43 | Village |
| Dawes township | 8 | 287 | 295 | 0% | 5 | 52.65 | Township |
| Flournoy township | 9 | 255 | 267 | -0.78% | 7 | 35.79 | Township |
| Perry township | 10 | 222 | 230 | 0% | 6 | 34.52 | Township |
| Rosalie | 11 | 149 | 156 | -0.67% | 760 | 0.20 | Village |
| Anderson township | 12 | 120 | 123 | 0% | 4 | 30.59 | Township |
| Thurston | 13 | 112 | 119 | -0.88% | 396 | 0.28 | Village |
| Thayer township | 14 | 104 | 108 | 0% | 4 | 23.85 | Township |
| Bryan township | 15 | 85 | 88 | 0% | 4 | 20.03 | Township |
| Merry township | 16 | 65 | 67 | 0% | 2 | 31.72 | Township |
Winnebago township is the largest city in Thurston County, with a population of 1,946.
Merry township is the smallest city in Thurston County.
There are 16 cities in Thurston County, Nebraska.