As a teenager, Funes was part of the youth divisions of Aurora F.C., debuting in the "Liga Mayor" with that team. He then joined Municipal – the club he would permanently be most identified with –, where he would reach the peak of his career. During his tenure with the "Rojos", Funes helped the team win three consecutive league titles in the 1987, 1988, and 1989-90 seasons, and two more in 1991-92 and 1993-94. He scored 43 goals in official tournaments for Municipal.