| Club: | Panathinaikos |
| Season: | 2012–13 |
| Chairman: |  Giannis Alafouzos |
| Manager: | Giannis Vonortas |
| League: | Super League Greece |
| League Result: | 6th |
| Cup1: | Greek Cup |
| Cup1 Result: | Round of 16 |
| Cup3: | Champions League |
| Cup3 Result: | Play-off round |
| Cup4: | Europa League |
| Cup4 Result: | Group stage |
| League Topscorer: | Toché (9) |
| Season Topscorer: | Toché (12) |
| Highest Attendance: | 27,719 (vs. Málaga, 28 August) |
| Lowest Attendance: | 1,730 (vs. Proodeftiki, 29 November) |
| Average Attendance: | 9,571 |
| Stdtitle: | Ground |
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| Prevseason: | 2011–12 |
| Nextseason: | 2013–14 |
The 2012–13 season is Panathinaikos' 54th consecutive season in Super League Greece.
They also competed in the Greek Cup. They were eliminated from the UEFA Champions League and the UEFA Europa League.
| Date | Pos. | Name | From | Fee | |
|---|---|---|---|---|---|
| 1 July 2012 | FW |  Kosta Barbarouses |  Alania Vladikavkaz | Loan | |
| 6 July 2012 | FW | Ibrahim Sissoko |  VfL Wolfsburg | Loan | |
| 6 July 2012 | MF |  Pape Sow |  Académica de Coimbra | Free | |
| 7 July 2012 | DF | André Pinto | Porto | Free | |
| 8 July 2012 | DF | José Manuel Velázquez |  Villarreal B | Free | |
| 20 July 2012 | FW |  Bruno Fornaroli |  Sampdoria | Free | |
| 14 August 2012 | FW |  Quincy Owusu-Abeyie |  Al Sadd | Free | |
| 1 January 2013 | MF |  Yohei Kajiyama | FC Tokyo | Loan | |
| 31 January 2013 | DF | Panagiotis Spyropoulos | Panionios | Free | |
| 31 January 2013 | FW | Thanasis Dinas | Panachaiki | Free | |
| 31 January 2013 | DF |  Nicky Kuiper | Twente | Loan | |
| 31 January 2013 | MF | Jokin Arcaya | Huesca | Free | |
| 11 February 2013 | FW |  Luciano Figueroa |  Emelec | Free |
| Date | Pos. | Name | To | Fee | |
|---|---|---|---|---|---|
| 1 July 2012 | FW |  Gergely Rudolf | Genoa | End of loan | |
| 1 July 2012 | MF |  Cleyton |  Kayserispor | Free | |
| 1 July 2012 | MF | Sotiris Ninis | Parma | Free | |
| 1 July 2012 | MF |  Simão Mate Junior |  Shandong Luneng Taishan | Free | |
| 1 July 2012 | MF |  Damien Plessis | Arles-Avignon | Free | |
| 1 July 2012 | MF | Sotiris Leontiou | Apollon Smyrnis | Free | |
| 1 July 2012 | MF | Giorgos Karagounis | Fulham | Free | |
| 1 July 2012 | DF | Christos Melissis | Panthrakikos | Free | |
| 1 July 2012 | DF |  Cédric Kanté | Sochaux | Free | |
| 1 July 2012 | DF |  Mattias Bjärsmyr | IFK Göteborg | Free | |
| 1 July 2012 | DF | Josu Sarriegi | Free | ||
| 30 August 2012 | DF | Giorgos Ioannidis | OFI | Free | |
| 1 October 2012 | MF | Kostas Katsouranis | PAOK | Free | |
| 1 January 2013 | FW | Antonis Petropoulos | AEK Athens | Free | |
| 21 January 2013 | FW | Sebastián Leto | Catania | Free | |
| 29 January 2013 | FW | Lazaros Christodoulopoulos | Bologna | Free | |
| 29 January 2013 | DF | Nikos Spyropoulos | Chievo | Free | |
| 30 January 2013 | DF | Loukas Vyntra | Levante | Free |
See main article: 2012–13 Super League Greece.
See main article: 2012–13 Greek Football Cup.
See main article: 2012–13 UEFA Champions League.
See main article: 2012–13 UEFA Champions League qualifying phase and play-off round.
See main article: 2012–13 UEFA Europa League.
See main article: 2012–13 UEFA Europa League group stage.