He moved frequently in his club career, representing teams in Portugal, Spain, Germany, Greece, Romania, the Netherlands, the United States, Norway and Malta.

The son of a Portuguese father and a Czechoslovakian mother,[2] Fernandes was born in Edmonton, Alberta,[3] being raised in East Vancouver, British Columbia.

Bundesliga side SSV Jahn Regensburg, but again failed to appear officially for the main squad, returning in June to Celta and being released from contract.

Despite many problems both inside and outside the pitch, PAOK managed to finish in sixth place in the 2005–06 campaign, with Fernandes making 27 appearances as the Thessaloniki club qualified for the UEFA Cup, only to be disqualified shortly after for irregularities.

On 23 May 2008, after extensive negotiations, PAOK accepted an offer from VfL Bochum, who signed Fernandes for a fee of approximately €1.2 million, with the player reuniting at the German side with former teammate Marcin Mięciel.

[12] Fernandes moved teams and countries again on 17 January 2012, signing a two-year contract with FC Twente in the Eredivisie and competing with Nikolay Mihaylov for the no.1 position.

[18] For the second consecutive time, Fernandes' American club folded, and he signed for Norwegian Eliteserien team Lillestrøm SK on a one-year deal in January 2017.

[21] On 1 July 2018, the 34-year-old Fernandes returned to Portuguese club football for the first time in 16 years, joining S.C. Farense for their upcoming season back in LigaPro.

In May of the following year, he was selected for a UEFA Euro 2008 qualifier against Belgium and a friendly with Kuwait,[30] making his debut in the latter after replacing Quim in the 66th minute of a 1–1 draw.