Zapata began his career with Millonarios, making his debut in the Colombian top flight during the 2001 season.

Since making his debut with Millonarios, Zapata was a regular starter at left back and was known primarily for his speed.

[3] After one season in Venezuela Zapata signed with Wilstermann of Bolivia for the clubs Copa Libertadores campaign.

In his first year at the club he helped Pasto in capturing the Primera B title and gain promotion to the Liga Postobón.

[5][6] After a three-week trial, Zapata signed with Colorado Rapids of Major League Soccer.