He started his career as a footballer in 1972, initially playing for SL Benfica at the youth level, and then Marítimo and GD Estoril-Praia where he ended his career.
Having an academic degree as a technical electronic engineer, in 1987 he decided to retire from football play and become a coach. His first Club was Estoril where he remained until 1994. With Fernando Santos as a coach, Estoril climbed up two categories and reached Portugal’s SuperLiga. In 1994 he took over Estrela da Amadora and in 1998 he moved to FC Porto. At the same year he won the Championship and Portugal’s Super Cup. He was the last of the coaches to win in FC Porto's run of 5 consecutive championships, the longest ever in Portuguese club history. For that, he is known as "the engineer of the penta". Next season Porto missed the 6th title in the last round to Sporting Lisbon but won the Portuguese Football Cup and Super Cup and reached the European Champions League quarter – finals.
In 2001 Fernando Santos took over AEK FC, leading the club to the conquest of Greek Football Cup but losing the Championship to Olympiakos due to goal average. His next step was Panathinaikos FC and then he was in charge of Sporting Clube de Portugal. He returned to AEK FC in order to continue the work he left behind. AEK FC based on young players reached the Greek Cup final and finished third (only three points behind the first) at the Greek First National Division. Fernando Santos returned to Portugal to coach Sport Lisboa e Benfica for the 2007 season. Afterwards, he returned to Greece, coaching PAOK Thessaloniki in the 2008 through 2010 seasons.
Following the end of the 2010 World Cup campaign of Greece, long-time coach, Otto Rehhagel, announced his resignation. The Hellenic Football Federation nominated Fernando Santos as his successor. Santos started his tenure as Greek coach with a 1-0 away win v. Serbia on August 11, 2010.
Career as a player
- Sport Lisboa e Benfica (at the youth level)
- GD Estoril-Praia
Career as a coach
- 1987-88 and 1989-94 GD Estoril-Praia
- 1994-95 and 1997-98 Estrela da Amadora
- 1998-01 FC Porto
- 2001-02 AEK FC
- 2002-03 Panathinaikos FC
- 2003-04 Sporting Clube de Portugal
- 2004-06 AEK FC
- 2006-07 SL Benfica
- 2007-10 PAOK FC
- 2010- National Football Team of Greece