Born in Lisbon, Silva finished his formation with local C.F. Os Belenenses. During a 15-year professional career he only appeared in two Primeira Liga games, one with that club and another with S.C. Campomaiorense; from 2000 to 2005 he alternated between the second and third divisions, representing C.D. Trofense, Rio Ave FC, S.C. Braga B, S.C. Salgueiros and Odivelas FC.
In the 2005 off-season, Silva joined G.D. Estoril Praia in the second level, where he remained until his retirement six years later, always in that tier. He played his last match on 2 January 2011, a 0–1 home loss against F.C. Penafiel for the campaign's Taça da Liga.
Silva retired in June at the age of nearly 34, amassing division two totals of 152 games and eight goals for three different clubs.
On 10 June 2011, immediately after retiring, Silva was appointed director of football at Estoril. However, early into the season, he replaced Vinícius Eutrópio as manager, with the Cascais team ranking tenth in the second tier. His first game in charge was a 1–3 defeat at Penafiel, and, after losing only three matches in 24, he helped the club return to the top flight after seven years, as champions. He ultimately was chosen the league's Manager of the Year.
Silva made his debut in the Portuguese top division on 17 August 2012, in a 1–2 away defeat to S.C. Olhanense. Estoril overachieved for a second best-ever fifth place in the table, with the subsequent qualification to the UEFA Europa League, also a first. Highlights included not losing any of the games against Sporting Clube de Portugal (3–1 at home, 2–2 away), and drawing at S.L. Benfica 1–1.
On 23 February 2014, Estoril achieved an historic first time win at the Estádio do Dragão, the 1–0 victory being FC Porto's first home defeat since the 2–3 against Leixões S.C. in 2008. He left his position on 12 May, after leading his team to the fourth position.
Silva agreed to a four-year contract with Sporting on 21 May 2014, replacing Leonardo Jardim who left for AS Monaco FC. He led the club to the third place in the championship, also winning the Taça de Portugal by beating S.C. Braga 3–1 on penalties after a 2–2 draw in the final. This was Sporting's first piece of silverware since the 2008 Supertaça Cândido de Oliveira.
On 4 June 2015, four days after winning the trophy, Sporting announced that Silva had been sacked with just cause, for not wearing the club's official suit in a cup match against F.C. Vizela.
On 8 July 2015, Silva was appointed the successor of countryman Vítor Pereira at Olympiacos FC, signing on a two-year contract. His first competitive game occurred in the season opener in the Superleague Greece, won 3–0 against Panionios FC. On 17 September, he played his first UEFA Champions League match with his new club, losing 0–3 at home to FC Bayern Munich.
Silva subsequently guided the team to break the record of 11 consecutive league wins from the first matchday, also recording a 3–2 success at Arsenal in the Champions League group stage. The Piraeus side's run of domestic wins ended at 17, a European record in the 21st century, but they nonetheless won a record 43rd title with six games remaining.
Silva quit his job on 23 June 2016, alleging personal reasons.
On 5 January 2017, Silva was appointed as the head coach of Hull City until the end of the season, replacing Mike Phelan who was sacked with the side bottom of the Premier League. Upon his appointment, club vice-chairman Ehab Allam said: "He has a great track record and we feel this is a bold and exciting appointment in our aim to retain the club's Premier League status". The former brought in his own coaching team, including assistant João Pedro Sousa, first-team coach Gonçalo Pedro and goalkeeping coach Hugo Oliveira.
Two days after his appointment, Silva coached Hull to a 2–0 win over Swansea City in the third round of the FA Cup. His first Premier League match in charge of the Tigers also ended in success; in a 3-1 victory over Bournemouth on 14 January.
On 26 January, Silva's Hull City defeated a Manchester United side coached by Portuguese compatriot José Mourinho 2–1 in the Football League Cup semi-final, giving the club its first victory over the Manchester club since 1974. However, due to United's 2–0 win in the first-leg of the tie, Hull failed to advance to the final. On 4 February, Hull beat Liverpool 2–0 in the Premier League, giving Silva four wins from his first four home matches as manager.
In March, Silva stated that he wanted to end the groundshare agreement with rugby league club Hull F.C. at the KCOM Stadium, as the latter played on Friday and affected the pitch quality for his team at the weekend.As of 18 March 2017
Segunda Liga: 2011–12
Taça de Portugal: 2014–15
Superleague Greece: 2015–16
Segunda Liga Coach of the Year: 2011–12