| Name | Address | Enrollment | Grade span |
|---|---|---|---|
| Fort Madison Alternative School | 1602 Avenue F, Ste. 1 | 74 | 9-12 |
| Fort Madison High School | 2001 Ave B | 706 | 9-12 |
| Fort Madison Middle School | 615 18th St | 511 | 6-8 |
| Holy Trinity Catholic Elementary-Fort Ma School | 509 Avenue F | 82 | 1-5 |
| Holy Trinity Early Childhood Center School | 2213 Avenue J | 64 | PK-K |
| Holy Trinity High School | 2600 Avenue A | 180 | 9-12 |
| Lincoln Elementary School | 1326 Ave E | 325 | K-5 |
| Richardson Elementary School | 3301 Avenue L | 439 | PK-5 |
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