[12] His first game in charge was a 3–1 defeat at Penafiel[13] and, after losing only three matches in 24, he helped the club return to the top flight after seven years, as champions.

[18] On 23 February 2014, Estoril achieved an historic first-time win at the Estádio do Dragão, the 1–0 victory – where he was sent off midway through the second half – being Porto's first home defeat since the 2–3 against Leixões in 2008.

On 4 June 2015, four days after winning the trophy, Sporting announced that Silva had been dismissed with just cause,[24][25] for not wearing their official suit in a cup match against Vizela.

[26] The dismissal was necessary for president Bruno de Carvalho to bring in Jorge Jesus from rivals Benfica, and included a clause requiring Silva to pay Sporting should he join another Portuguese team.

On 16 September, he played his first UEFA Champions League match with his new club, losing 0–3 at home to Bayern Munich in the group stage.

[35] 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 dismissed with the team bottom of the Premier League.

[39] On 26 January 2017, Silva's Hull beat Manchester United 2–1 in the semi-finals of the EFL Cup, giving the club its first victory over that opponent since 1974.

[45] During this period and in the subsequent two months, the team's performances became increasingly poor (five points from 30 in ten Premier League matches), with fans citing his loss of focus as putting them at risk of relegation.

[61][62] On 1 July 2021, Silva was appointed as head coach at recently relegated Championship club Fulham on a three-year contract, after Scott Parker had left to join Bournemouth.

[66] On 19 April, the side secured an immediate return to the top division after a 3–0 win over Preston North End,[67] confirming the league title two weeks later after beating Luton Town 7–0 and totalling 106 goals, a competition-best after Manchester City's 108 in 2001–02.

[68][69][70] Silva apologised after being sent off due to improper conduct during a 3–1 defeat away to Manchester United in the FA Cup quarter-finals on 19 March 2023, following the dismissal of his player Willian for handball.

[76] On 19 December, he led Fulham to their first ever League Cup semi-final, beating Everton on penalties[77] before bowing out to Liverpool 3–2 on aggregate.