Fernandes started his senior career at 18 with Italian Serie B side Novara but soon made a move to Serie A side Udinese, followed by Sampdoria three years later.
After five years in Italy, he signed with Sporting CP.
He won back-to-back Taças da Liga in 2018 and 2019, as well as the Taça de Portugal, leading to him being named Primeira Liga Player of the Year in both seasons.
In 2018–19, he scored a record of 33 goals in all competitions, making him the highest-scoring Portuguese midfielder and the highest-scoring midfielder in Europe in a single season.
Fernandes' performances sparked the interest of Premier League clubs. Manchester United signed him for an initial €55 million (£47 million) in January 2020.
In June 2020, he won multiple club and Premier League awards, including Premier League Player of the Month and Goal of the Month, becoming the first player to win both awards concurrently in Premier League history.