Born in Cali of Lebanese descent, Mondragón began his career began at Deportivo Cali, and he moved to Independiente Santa Fe and then Cerro Porteño in Paraguay. His career took off when he joined the Argentine first division side Argentinos Juniors in 1993, and then made his international debut for Colombia. The following year he moved to Club Atlético Independiente where he won, among other titles, the 1995 Supercopa Libertadores against Flamengo. Apart from some brief periods, he largely stood at the club until 2001.