Fernandes was selected by FC Goa in the 2017 ISL draft.
In his first season as a Gaur, the forward-cum-winger accounted for 2 goals and 4 assists over 17 games in all competitions as the club reached the semis in both the Indian Super League and the Super Cup.
Brandon had his best season in 2018/19 when he featured in 22 games for FC Goa.
His 6 goals and 6 assists across all competitions helped the Gaurs reach the final of the Indian Super League before lifting the Super Cup in April with Brandon scoring the eventual winner in the final.
"Frankly, I just love playing for this club, playing for Goa. I would like to thank Sergio Lobera and the management at the club for believing in me and helping me take my game to the next level," Fernandes was quoted as saying in the release.
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