[4] After spending time with Velsao Pale, Fernandes moved to the Goa United Football Academy before being signed by Salgaocar to join their under-14 side.

[4] After impressive performances for both Salgaocar and the India under-20 side, Brandon was enrolled into the ASD Football Academy in Cape Town, South Africa.

Fernandes also played for the ASD Cape Town team in the SAFA Second Division, the third-tier of South African football, where he managed to score 12 goals from 12 matches, 4 of which were free-kicks.

[1] A year after his contract with ASD Cape Town expired, and after saying in the past that he would not play in the I-League, Fernandes returned to India to sign for Sporting Goa.

[11] Brandon scored his first senior professional goal against Salgaocar on 19 April 2015 in a 2–0 win for Sporting Goa[12] Fernandes then put in a man of the match performance over Bharat on 2 May 2015.

[13] After the match, Fernandes was praised by Sporting Goa head coach, Mateus Costa, when he said that "Since Brandon joined our squad, things have really changed.

Pouncing on a mistake by Shillong Lajong goalkeeper, Rehenesh TP, in which the keeper miss kicked his clearance, Brandon slotted the ball into the net from more than 30 yards out.

[28] During the 2018–19 season, Brandon was an integral part of the Sergio Lobera's system, playing primarily on the left side of midfield as his team finished second the league on head-to-head ruling.

[30] On 20 April 2021, Fernandes assisted Edu Bedia to score the first ever goal by an Indian club in the AFC Champions League's group stage, despite his team losing the game against Persepolis.

[32] He made his second debut for the club in their first league match of the season, away against Mohun Bagan SG as an 85th-minute substitute for Jeremy Manzorro,[33] as Mumbai went on to fight back from 2-0 down to draw the game 2-2.

Many fans criticised the decision of the coach to snub the likes of Brandon Fernandez, Rahul Bheke, Sosairaj, Mandar, Adil who have been performing well for the last 2–3 seasons for the AFC Asian Cup 2019.

[35] He played in the final of the tournament, assisting twice and scoring once from the penalty spot, as Goa beat the under-20 team of Mozambique to become the champions at the Lusophony Games.