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. Upon his appointment, 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". Silva brought in his own coaching team, including assistant João Pedro Sousa, first-team coach Gonçalo Pedro and goalkeeping coach Hugo Oliveira.
On 26 January 2017, Silva's Hull defeated a Manchester United team, coached by Portuguese compatriot José Mourinho, 2–1 in the semi-finals of the EFL Cup, giving the club its first victory over that opponent since 1974. However, due to the latter's 2–0 win in the first-leg of the tie, the former failed to advance to the final, but on 4 February they beat Liverpool 2–0 in the domestic league, giving the coach four wins from his first four home matches as manager.
In March 2017, 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. On 25 May, after the team's relegation, he resigned.
On 27 May 2017, it was confirmed Silva would join Premier League club Watford as head coach on a two-year contract. After a good start to the season, he was tracked for the vacant managerial position at Everton in November. 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.