The2015–16 Querétaro F.C. season was the club's 66th season of existence, and their 15th season in the top tier of Mexican football.Querétaro competed inLiga MX and theCONCACAF Champions League.
Note: Flags indicate national team as defined underFIFA eligibility rules; some limited exceptions apply. Players may hold more than one non-FIFA nationality.
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| 8 January 20161 | Querétaro | 1–3 | Atlas | Querétaro City |
| Stadium:Estadio Corregidora |
| 22 January 20163 | Querétaro | 3–0 | Dorados | Querétaro City |
| Stadium:Estadio Corregidora |
| 29 January 20164 | Santos Laguna | 2–0 | Querétaro | Torreón |
| Stadium:Estadio Corona |
| 5 February 20165 | Querétaro | 2–1 | Veracruz | Querétaro City |
| Stadium:Estadio Corregidora |
| 13 February 20166 | Cruz Azul | 2–1 | Querétaro | Mexico City |
| Stadium:Estadio Azul |
| 19 February 20167 | Querétaro | 2–2 | Tigres UANL | Querétaro City |
| 20:30 | Forlín 45'Jiménez 48' | Report | Gignac 12' Aquino 50' | Stadium:Estadio Corregidora Referee: Diego Montaño |
| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts | Qualification |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 |  Querétaro | 4 | 2 | 1 | 1 | 11 | 2 | +9 | 7 | Knockout stage |
| 2 |  San Francisco | 4 | 2 | 0 | 2 | 11 | 5 | +6 | 6 | |
| 3 |  Verdes | 4 | 1 | 1 | 2 | 2 | 17 | −15 | 4 |
vSan Francisco| 4 August 20151 | Querétaro | 2–0 | San Francisco | Querétaro City |
| 20:00EDT | Villa 61' Milke 76' | Report | Stadium:Estadio Corregidora |
vQuerétaro| 18 August 20152 | Verdes | 0–0 | Querétaro | Belmopan |
| 20:00EDT | Report | Stadium:FFB Stadium Referee:Valdin Legister (Jamaica) |
vQuerétaro| 26 August 20153 | San Francisco | 2–1 | Querétaro | Panama City |
| 20:00EDT | Rodríguez 89' Alfaro 90' | Report | Sinha 76' | Stadium:Estadio Maracaná Referee:Walter López (Guatemala) |
vVerdes| 26 August 20153 | Querétaro | 8–0 | Verdes | Querétaro City |
| 22:00 | Gutiérrez 15' Villa 30',51',53',85',90'Sinha 81'Danilinho 86' | Report | Stadium:Estadio Corregidora Referee:Elmer Bonilla (El Salvador) |
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D.C. United| 23 February 2016First leg | Querétaro | 2–0 | D.C. United | Querétaro City |
| 20:00EDT | Candelo 71' Benítez 83' | Summary | Sarvas 73' | Stadium:Estadio Corregidora Referee: Ramón Hernández |
vQuerétaro| 1 March 2016Second leg | D.C. United | 1–1 (1–3agg.) | Querétaro | Washington, D.C. |
| 20:00EDT | Sarvas 12' Boswell 72'Büscher 84' | Stadium:RFK Stadium Attendance: 10,790 |
vUANL| 16 March 2016First leg | Querétaro | 0–0 | UANL | Querétaro City |
| 20:00EDT | Stadium:Estadio Corregidora |
vQuerétaro| 6 April 2016Second leg | UANL | 2–0 (2–0agg.) | Querétaro | San Nicolás de los Garza |
| 20:00EDT | Stadium:Estadio Universitario |
