Born in Taquaritinga, São Paulo, Edmílson signed for São Paulo FC in 1994, winning the Campeonato Paulista titles in 1998 and 2000, adding the 1994 Copa CONMEBOL and the subsequent Recopa Sudamericana.
Edmílson recovered fully for 2005-06, playing an important part in Frank Rijkaard's team as they won the league and the season's UEFA Champions League.