Querétaro FC (Liga MX Clausura): every transfer in and out, fees paid and earned, squad market value, €6.9m spent and €26m earned.
| Date | Player | From | To | Fee |
|---|---|---|---|---|
| 2026-09-01 | Alan Medina | Querétaro FC | UNAM Pumas | — |
| 2026-07-01 | Santiago Homenchenko | Pachuca | Querétaro FC | €3.5m |
| 2026-07-01 | Luis Villegas | Querétaro FC | Without Club | — |
| 2026-07-01 | Luis Gutiérrez | Querétaro FC | Without Club | — |
| 2026-07-01 | Lucas Rodríguez | Querétaro FC | Without Club | — |
| 2026-07-01 | Jhojan Julio | Querétaro FC | Without Club | — |
| 2026-07-01 | Jaime Gómez | Querétaro FC | Without Club | — |
| 2026-07-01 | Fernando González | Querétaro FC | Without Club | — |
| 2026-07-01 | Eduardo Armenta | Querétaro FC | Without Club | — |
| 2026-01-14 | Martín Río | Querétaro FC | Banfield | €549k |
| 2026-01-13 | Bernardo Parra | Tigres UANL | Querétaro FC | — |
| 2026-01-09 | Aldahir Pérez | Querétaro FC | Club Tijuana | — |
| 2026-01-07 | Waldo Madrid | Necaxa U21 | Querétaro FC | Loan |
| 2026-01-01 | Óscar Manzanárez | Querétaro FC | Club Tijuana | — |
| 2026-01-01 | Érik Dueñas | Houston | Querétaro FC | Free |
| 2026-01-01 | Ángel Zapata | Querétaro FC | Club Tijuana | — |
| 2026-01-01 | Álex Alcalá | Man City U21 | Querétaro FC | Free |
| 2026-01-01 | Lucas Abascia | Ñublense | Querétaro FC | Free |
| 2026-01-01 | Jesús Arellano | Querétaro U21 | Querétaro FC | — |
| 2026-01-01 | Jean Unjanque | Cancún FC | Querétaro FC | Loan |