Serginho initially began his professional footballing career in his home-country, and played for clubs Cruzeiro EC, Bahia, and São Paulo FC. He moved to Italian side A.C. Milan in 1999, where he was initially a fringe player, starting on the bench but often being the first-choice substitute. The apex of Serginho's Milan career was when he scored a goal and contributed three assists in a 6–0 thrashing of crosstown rivals Internazionale on 11 May 2001. He also contributed to Milan's 2003 UEFA Champions League victory over Juventus, scoring the first of Milan's three successful penalties in the shootout. The 2005 Champions League Final was a reversal of fortune, however, as Milan surrendered a 3–0 lead at half-time and eventually lost on penalties to Liverpool, with Serginho whistling his shot over the crossbar. Serginho also won the 2003–04 Serie A title with Milan and the 2006–07 edition of the UEFA Champions League, among other trophies.