| Club: | Villarreal |
| Season: | 2012–13 |
| Chrtitle: | President |
| Chairman: | Fernando Roig |
| Mgrtitle: | Head coach |
| Manager: | Julio Velázquez (until 13 January) Marcelino (from 14 January) |
| Stadium: | El Madrigal |
| League: | Segunda División |
| League Result: | 2nd (promoted) |
| Cup1: | Copa del Rey |
| Cup1 Result: | Second round |
| League Topscorer: | Ikechukwu Uche (14) |
| Season Topscorer: | Ikechukwu Uche (14) |
| Pattern La1: | _villarreal1213h |
| Pattern B1: | _villarreal1213h |
| Pattern Ra1: | _villarreal1213h |
| Leftarm1: | FFFF00 |
| Body1: | FFFF00 |
| Rightarm1: | FFFF00 |
| Shorts1: | FFFF00 |
| Socks1: | FFFF00 |
| Pattern La2: | _villarreal1213a |
| Pattern B2: | _villarreal1213a |
| Pattern Ra2: | _villarreal1213a |
| Leftarm2: | 000064 |
| Body2: | 000064 |
| Rightarm2: | 000064 |
| Shorts2: | 000040 |
| Socks2: | 000040 |
| Prevseason: | 2011–12 |
| Nextseason: | 2013–14 |
The 2012–13 season was Villarreal Club de Fútbol's 90th season in existence and the club's first season back in the second division of Spanish football following relegation at the end of the 2011–12 La Liga season. In addition to the domestic league, Villarreal participated in this season's edition of the Copa del Rey. The season covered the period from 1 July 2012 to 30 June 2013.
See main article: 2012–13 Segunda División.
See main article: 2011–12 Copa del Rey.
The numbers are established according to the official website:https://web.archive.org/web/20150814033410/http://villarrealcf.es/es/primer-equipo/plantilla and www.lfp.es
| Date | Pos. | Name | From | Fee | |
|---|---|---|---|---|---|
| 13 June 2012 | DEF |  Javi Venta | Levante | Free[1] | |
| 13 May 2012 | DEF | Iván Marcano | Olympiacos | Loan return | |
| 13 May 2012 | MID |  Jefferson Montero | Real Betis | Loan return | |
| 13 May 2012 | FW |  Ikechukwu Uche | Granada | Loan return | |
| 13 May 2012 | GK | Juan Carlos | Elche | Loan return | |
| 8 August 2012 | DEF |  Olof Mellberg | Olympiacos | Free[2] |
| Date | Pos. | Name | To | Fee | |
|---|---|---|---|---|---|
| 22 May 2012 | GK | Diego López | Sevilla | €3.5M[3] | |
| 2 June 2012 | DEF | Iván Marcano |  Rubin Kazan | €5M[4] | |
| 17 June 2012 | MID | Jefferson Montero |  Monarcas Morelia | Undisclosed[5] | |
| 17 July 2012 | FW |  Nilmar |  Al-Rayyan | Undisclosed[6] | |
| 12 July 2012 | MID |  Mubarak Wakaso | Espanyol | Undisclosed[7] | |
| 13 July 2012 | FW |  Marco Ruben |  Dynamo Kyiv | Undisclosed[8] | |
| 1 June 2012 | GK | César | Retirement | Free | |
| 3 June 2012 | FW | Alejandro Martinuccio | Fluminense | Loan return | |
| 1 August 2012 | MID | Borja Valero |  Fiorentina | €7M[9] | |
| 1 June 2012 | DEF | Carlos Marchena | Deportivo La Coruña | Free | |
| 2 August 2012 | DEF | Gonzalo Rodríguez | Fiorentina | Undisclosed[10] | |
| 1 July 2012 | MID | Gonzalo Castellani | Godoy Cruz | Undisclosed[11] | |
| 9 August 2012 | DEF | Ángel López | Free agent | Free | |
| 4 January 2013 | FW | Giuseppe Rossi | Fiorentina | €9.5M |
| Date from | Date to | Pos. | Name | To | ||
|---|---|---|---|---|---|---|
| 1 July 2012 | 15 May 2013 | FW | Joselu | Córdoba | Loan[12] | |
| 10 July 2012 | 15 May 2013 | MID | Jonathan de Guzmán | Swansea City | Loan | |
| 8 August 2012 | 15 May 2013 | DEF |  Cristián Zapata | Milan | Loan[13] |