Fotakis spent his early career in his native Greece, playing for PAOK, Kallithea and Egaleo. He moved to Scotland in January 2006 to sign for Kilmarnock, but he never made a league appearance for them. He then returned to Greece in 2006 with Larissa, before moving to PAOK in the summer of 2009. He played with PAOK for four consecutive years, before he moved for a 1+1 year contact to Şanlıurfaspor. At January 31st,2014 he signed with Atromitos a one and a half year contract. On May 27,2014 Atromitos announced the end of cooperation with Fotakis.  On August 31,2015 Fotakis signed with Panetolikos for a year contract.