Fonseca, nicknamed el castor ("the beaver"), started his football career at Nacional, his local team in Uruguay, in 1988. He played 14 games in two years and scored 3 goals, winning the South American Cup Winners Cup whilst there.
In 1990, he moved to Cagliari, scoring 17 goals in 50 appearances, playing mostly on the left than in the centre.
In 1992 Napoli signed him and Fonseca managed a more impressive strike rate, scoring 31 goals in two seasons in Naples, including 5 goals against Valencia in the UEFA cup. This form brought attention from A.S. Roma, who promptly signed him in 1994.
However, his three seasons (from 1994 to 1997) were far from successful. He played as a second striker supporting the Argentine centre forward Abel Balbo, but, because of the many injuries he suffered, he played discontinuously.
Juventus signed Fonseca in 1997, but again was played out of position on the left as he had been at Napoli. His goalscoring record in Serie A was very good considering he was not always first choice at AS Roma and at Juventus. Fonseca was always regarded as a super sub and scored important goals coming off the bench. He won two Serie A titles, a Champions League runner-up medal and the Supercoppa Italiana whilst there.
Injury ruled him completely out of the 1999-2000 season, which saw him transferred to River Plate in Argentina. There, he infamously played only during the club's 2000 pre-season. His only match was a pre-season encounter against archrivals Boca Juniors, earning a win by scoring the final penalty in the shootout. A few days later, Fonseca would resign from his contract and join Como in 2001. He retired in 2003 after the coach said he wasn't in his first team plans .