Eduardo da Silva was on the books of Dinamo Zagreb when he spent one season at fellow Croatian side Inter Zapresic. The Brazilian-born Croatian striker made his debut for Dinamo Zagreb during the 2001/02 season before he was loaned to Inter Zapresic for one season. Eduardo da Silva was at Inter Zapresic for the entire duration of the 2002/03 season.

At Inter Zapresic, Eduardo became a first-team regular for the first time in his young professional career. He was able to reach double figures in the league during his time at Zapresic. He scored ten goals in 15 appearances in the league during his time at the club.

On his return to Dinamo Zagreb from his loan spell at Inter Zapresic, Eduardo da Silva became a regular in the starting XI as he established himself in the team. Also, he was rewarded for his form with the best player award when he returned to Dinamo Zagreb. The striker was named the best player for the 2004/05 season. He would later repeat for the 2005/06 and 2006/07 seasons. Eduardo da Silva was a key player as Dinamo Zagreb won successive league titles plus one Croatian Cup title. He also scored a brace in the Croatian Super Cup in 2006 which ended in a 4-1 win over Rijeka.

During the 2006/07 season, Eduardo scored five times in six games on the European scene over the two Champions League qualifying round and the UEFA Cup first round.He scored twice in the 4-1 away win over Ekranasbefore netting the first European goal at the new Emirates Stadium as Dinamo Zagreb suffered a 5-1 aggregate defeat to Arsenal in the Champions League third qualifying round. Eduardo da Silva also scored twice during the 5-2 aggregate win over French team Auxerre in the UEFA Cup first round.