The 2012–13 season is Atalanta Bergamasca Calcio's hundred and fifth season in existence and the club's second consecutive season in the top flight of Italian football.

The club was punished with a two-point deduction plus a €25,000 fine at the start of the season, due to involvement in the 2011–12 Italian football scandal.

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

Players may hold more than one non-FIFA nationality.

The list is sorted by shirt number when total goals are equal.