Gan began playing football for his local club, Marton Hammers before signing for the Sutherland Sharks in 2000 when he was twelve years old, progressing through their youth grades to make his senior debut for the club in 2008. He made 15 league appearances scoring 6 goals, and 3 appearances in the Finals Series.[1] It was this debut season that shot Gan to prominence within the local media which brought with it a growing reputation to match.[2] His performances eventually led to his being crowned the New South Wales Premier League player of the year, winning the Gold Medal award for the competition.[3]
Sydney FC
Gan was than signed by Sydney FC for their inaugural National Youth League squad ahead of competition from rival A-League clubs.[4][5] On 28 November 2008, he made his debut for Sydney FC against Queensland Roar with a 5-minute cameo where he turned heads.[6][7] On 7 December, he scored the winning goal in the 78th minute for Sydney FC against Newcastle Jets to give them their first win in 7 games.[8]
Gan was given his full senior debut on 13 December against the Central Coast Mariners.[9] He scored his second senior goal against Melbourne Victory with a long range strike from outside the penalty area.[10] Brendan scored his third senior goal against Wellington Phoenix with a powerful header from a corner. This goal gave Sydney FC a 2–0 win over Wellington and placed them on the top of the table, leapfrogging Gold Coast United. On 2 December 2010, in only his second start for the season, he scored the opening goal in a 3–1 win, once again against Wellington Phoenix. He was released from Sydney, along with several other players at the end of Sydney's 2011 AFC Champions League campaign.[11]
On 17 November 2011, Gan moved to Malaysian club, Sabah as one of the two foreign players allowed in the 2012 Malaysia Super League. Brendan, alongside his fellow countrymen, Michael Baird signed a one-year contract with Sabah.[14]
In November 2013, Gan returned to Malaysia and signed a three-year contract with Malaysia Super League club Kelantan ahead of the 2014 season. He was supposed to be registered as a local player for Kelantan but did not get the approval from FAM because according to FAM, any player to be registered as a local player is required to have Malaysian identity card or passport. On 6 April, he officially obtained an identity card as a Malaysian and was registered by Kelantan as a local player during the April 2014 transfer window.[16][17][18][19]
Gan made his debut during the match between Kelantan against Terengganu which ended 1–1. In the first match of the 2015 Malaysia Super League, Gan suffered a serious torn ACL in his right knee that would keep him out for most of the 2015 season.[20] In September 2016, Brendan suffered another ACL injury, this time in his left knee which keep him out for 10 months, ruling him out for the 2016 AFF Championship where he was released by the club at the end of 2016.[21]
Perak FA
After making his recovery from a long term ACL injury, On 15 December 2017, Gan signed with Perak.[citation needed] On 24 February 2018, Gan played his first football match in over a year during a league match against Pahang FA. He would than played in the club 2019 AFC Champions Leaguepreliminary round 2 match against Hong Kong club, Kitchee where he played the entire 120th minute helping the club to progress to the final play-off round against Korean Ulsan Hyundai. On 8 February 2019, he scored his first goal for the club in a 1–1 draw against Kedah FA.[citation needed]
Selangor
On 1 December 2019, Gan officially joined Malaysia Super League club Selangor. In July 2021, Gan was diagnosed with testicular cancer and missed the rest of season.[22][23] In June 2022, he made his return in a 7–0 over Sarawak United, scoring a brace.[24] He was appointed as Selangor's captain since 2021. At the end of the 2023 Malaysia Super League season, Selangor confirmed Gan's departure with them after spending four seasons together.[citation needed]