The 2012–13 season was Olympiacos' 54th consecutive season in the Superleague Greece. They competed in the Greek Superleague, Greek Cup, UEFA Champions League and UEFA Europa League.

Olympiacos completed a domestic double, winning the Superleague and the Greek Cup. Olympiacos won the title for a third consecutive season, reaching 40 domestic titles and therefore adding a fourth star to the team's shirt.

The club finished third in Group B of the Champions League, which resulted in them entering the Europa League. Olympiacos was eliminated in Round of 32 by Levante with two defeats, falling 0–4 on aggregate.

As of 7 April 2013 Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

In: Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

Out: Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

In: Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

Out: Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

Source: Super League Greece
Rules for classification: 1) points, 2) head-to-head points, 3) head-to-head goal difference.
If in current league table there are tied teams after applying criteria 1 to 3, they are considered to share places and listed in Greek language alphabetic order.
If in final league table there are still tied teams after applying criteria 1 to 3, a decision match (or matches if they are more than two) are to be played but only in three cases: to determine the champion, to fill spots in the play-off or to determine the teams to be relegated. In any other case, the final standings of tied teams are determined with a public draw
¹Panathinaikos started the league season with minus 2 points because of severe crowd violence during their home match against Olympiacos last year.
²AEK Athens were deducted 3 points because of severe crowd violence during their home match against Panthrakikos this year.
(C) = Champion; (R) = Relegated; (P) = Promoted; (E) = Eliminated; (O) = Play-off winner; (A) = Advances to a further round.
Only applicable when the season is not finished:
(Q) = Qualified to the phase of tournament indicated; (TQ) = Qualified to tournament, but not yet to the particular phase indicated; (RQ) = Qualified to the relegation tournament indicated; (DQ) = Disqualified from tournament.

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