After spending two years at Dempo, during which Fernandes was used as a player in the Goa Professional League and in three AFC Cup matches in 2011, he signed for Mumbai F.C. of the I-League on 7 June 2012.
Fernandes made his debut for Churchill Brothers in the I-League on 21 September2013 against Salgaocar at the Duler Stadium, coming on as a substitute for Alesh Sawant in the 65th minute. Churchill Brothers lost the match 1–0.