After also playing youth football there he was promoted to local powerhouse C.S.
Marítimo's first team for the 1999–2000 season, but served only as a backup for the vast majority of his 12-year spell.
Estrela da Amadora, Fernando scored the club's historical 1,000 goal in the Primeira Liga.
Fernando played a combined 23 league matches for Marítimo in the following three years – no appearances whatsoever in 2010–11 – continuing to feature for the reserves sporadically.
At the age of 30 he moved abroad for the first time, signing with C.R.D.