In the 2003–04 season Panathinaikos played for 45th consecutive time in Greece's top division, Alpha Ethniki.

They also competed in UEFA Champions League, UEFA Cup and Greek Cup.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

Players may hold more than one non-FIFA nationality.

Panathinaikos qualified to the Round of 16 without a match.