Born in Lisbon, Fernandes grew up in the capital suburb of Amadora, where he would regularly play street football with future Sporting CP and Manchester United star Nani as a child.

Benfica's youth system and made his first-team debut during the 2003–04 season under coach José Antonio Camacho, making an immediate impression on both the manager and the club's supporters and becoming its second youngest ever goalscorer in only his second game, a 2–1 away win against Gil Vicente FC.

In the summer of 2006, Fernandes signed for Portsmouth of the Premier League on loan, with a deal agreed for a permanent transfer of approximately £7 million if he fully recovered from his groin injury.

[12] He also signed a long-term contract with Benfica in January 2007,[13] the deal being complicated due to the fact he was part-owned by a third party agency,[14] but he eventually made an assured debut for his new club in the 1–0 win over Blackburn Rovers on 10 February,[15] and quickly became something of a fans' favourite at Goodison Park; he scored his first league goal for the club on 24 February against Watford[16] and, on 28 April, added another against league leaders Manchester United – the goal, although spectacular, was not enough as the opposition would go on to score four times in the final half-hour of the game, winning 4–2.

[26] On 5 October 2008 he scored the only goal in a win at Real Valladolid, his first with the club;[27] overall, during his first full campaign, he complemented well with veterans David Albelda and Rubén Baraja, totalling 27 games and 1,718 minutes, but also sustained a fibula injury against Getafe CF in April 2009 even though he played the entire match.

[28] In January 2010, Fernandes was expected to sign on loan with Inter Milan due to lack of opportunities at Valencia, with the Italians having the right to buy off his contract at the end of the season.

[30] He appeared in a total of 20 competitive games during his first spell in Istanbul (14 in the league, six in the cup) and, in early July 2011, a permanent three-year contract was arranged for a €2 million transfer fee.

Sporting director Kirill Kotov referred to the player's "perfect technique and high playing intellect" as being the main reasons for his acquisition in order "to boost creativity in midfield".

[34] On 28 September 2017, Fernandes became the fastest-ever player to score a hat-trick in the history of the UEFA Europa League, achieving the feat in 17 minutes to help the hosts defeat FC Fastav Zlín 3–0 in the group stage.

[40] In June 2007, Fernandes played in all games at the UEFA European Under-21 Championship, scoring the opening goal for Portugal in their 4–0 win over Israel – the national side eventually failed Olympic qualification.

[42] He scored his first senior international goal on 26 March in a friendly match with Canada,[43] and played his first official game against Armenia on 17 November 2007, a 1–0 win in Leiria for the UEFA Euro 2008 qualifiers.