Along with Khairul Amri, Shahril Ishak and Hassan Sunny, Baihakki was in the pioneer batch of the National Football Academy in 2000.

He is recognised as one of the best centre-backs in the region with his tough tackling no nonsense approach often putting fear into opposition forwards.

In the National Football Academy age-group squads, he caught the eye with his 1.91 m stature, instinctive confidence and composure at the back.

In 2008, he return to his previous club but again, his army conscription clashed with his football career, and thus he missed the first few games of the new season for his new team, Geylang United.

In a controversial decision, Baihakki left Persija Jakarta for fierce rivals, Persib Bandung at the end of the 2009-10 Indonesia Super League season.

[4][5] On 16 February 2011, Baihakki signed a two-year deal with Medan Chiefs worth approximately US$300,000, along with Shahril Ishak,[6] who was also released by Persib.

In 2014, Baihakki signed a four-year contract with Malaysian Super League team, Johor Darul Takzim.

[8] After a series of unimpressive performances, he was de-registered from the squad on 18 April 2014 and replaced with Marcos Antonio Elias Santos.

He went for a trial with Saudi Arabian second-tier side, Jeddah Club after he was set up by his agent while on an Umrah pilgrimage trip with his family.

[13] However, a last minute deal was offered to him to play in the Thai League 1 and on 26 January 2018, he signed a contract with 4 time-league winner, Muangthong United ahead of the 2018 season.

[13] After signing with Muangthong United, On 5 February 2018, Baihakki was immediately loaned out to Thai League 2 side, Udon Thani.

Under the terms of the contract, Baihakki would play for free this season, should the 2020 Singapore Premier League resume after being suspended due to the COVID-19 pandemic.

Then captain of the Under-23 team, he led the Young Lions out for the 2005 Southeast Asian Games in Philippines and also won a bronze medal for the 2007 edition in Korat, Thailand.

He played his last final match for Singapore on 11 June 2021 against Saudi Arabia at the King Saud University Stadium in Riyadh.