In May 2014, Silva became the head coach of Sporting. In the 2014/15 season, the team under his leadership took third place in the championship and won the Portuguese Cup, the club's first trophy since 2008. However, in the summer of 2015, he was fired after an incident with a refusal to wear an official club suit to a Portuguese Cup match, which allowed the club to invite a new coach.
In July 2015, Silva took over the Hellenic Olympiacos. In his first season, he led the team to the 2015/16 Greek Super League title, setting a record of 17 consecutive league wins, which became a 21st century European record. Also, under his leadership, Olympiacos defeated Arsenal in the Champions League. In June 2016, he left the club for personal reasons.
In January 2017, Silva became the head coach of Hull City, which was in the relegation zone in the Premier League. Despite the improvement in the game, the team was eliminated, and the coach left the post.
On May 31, 2018, he became the head coach of Everton. Under his leadership, the team showed improvement, but in December 2019, he was fired.
On July 1, 2021, Silva took over Fulham, which had just been relegated to the Championship. In the 2021/22 season, he led the team to the Championship title and a return to the Premier League.