He amassed Primeira Liga totals of 111 games and three goals over the course of seven seasons, most notably with Estrela da Amadora. In 2005, he became a manager.
Born in Nampula, Portuguese Mozambique, Fonseca played 14 years as a senior, beginning with F.C. Barreirense in the third division and moving straight to the Primeira Liga with Leça F.C. in the 1995–96 season, starting in 21 of his league appearances as the club finished 14th and narrowly avoided relegation. In the following five years he continued in the latter competition, being first-choice with C.F. Os Belenenses and C.S. Marítimo but only a backup with Vitória S.C. and C.F. Estrela da Amadora.
Fonseca retired in June 2005 at the age of 32 after a further four campaigns with Estrela, three of those spent in the second level. In the 2003–04 campaign he participated in 15 games as the Lisbon side ranked dead last in the main category, with the subsequent relegation.
Fonseca started coaching immediately after retiring, remaining two years at the helm of Estrela da Amadora's youth team. From 2007 to 2011 he was in charge of several modest teams, notably C.D. Pinhalnovense, which he led to the quarter-finals of the Taça de Portugal in both the 2009–10 and 2010–11 seasons.
In 2011–12, Fonseca was appointed at C.D. Aves in division two for his first job in the professionals, and he led the team to the third position, just two points shy of promotion. In the following campaign he signed for F.C. Paços de Ferreira, repeating the position and subsequently qualifying the club to the UEFA Champions League for the first time in its history; highlights included winning both games against S.C. Braga (2–0 at home, 3–2 away) and Sporting Clube de Portugal (1–0 on both occasions).
Fonseca succeeded Vítor Pereira at the helm of back-to-back-to-back national champions FC Porto, signing a two-year contract on 10 June 2013. He started his spell on a high note, winning the year's Supertaça Cândido de Oliveira after a 3–0 triumph against Vitória de Guimarães.
However, on 5 March 2014, following a string of poor results that left the club in the third position in the league, nine points behind leaders S.L. Benfica, he was relieved of his duties. Previously, on 12 January, he had stated that Porto would be champions in the last matchday against Benfica.
From 2014 to 2016, Fonseca continued working in his country's top flight, with Paços and S.C. Braga. He led the latter to the fourth position, also winning the domestic cup.
On 31 May 2016, Fonseca moved abroad for the first time in his career, replacing legendary Mircea Lucescu (12 seasons) at the helm of FC Shakhtar Donetsk and signing a two-year contract at the Ukrainian Premier League side.As of 19 August 2017
Supertaça Cândido de Oliveira: 2013
Taça de Portugal: 2015–16
Ukrainian Premier League: 2016–17
Ukrainian Cup: 2016–17
Ukrainian Super Cup: 2017
Ukrainian Premier League: Best Coach 2016–17