The club represents the state of Sabah in Borneo, and competes in the Malaysia Super League, the top tier of Malaysian football.

[5] Sabah was a well known team during the Malaysian football amateur and semi-pro era and produced many quality players, namely the trio of James Wong, Hassan Sani and Peter Rajah.

Quality players were produced from the ranks during the 1990s, most notably Matlan who helped Sabah finish as runners-up during 1993 and 1994 Malaysia FA Cup, and who at one time was appointed as the national team captain by Claude Le Roy.

As a punishment for their involvement in match fixing, he and the other players were banned for life by FIFA and banished from the state of Sabah under the Restricted Residence Act.

[12] The 2000 season could be considered as Sabah's worst since joining the Malaysian professional league as they were relegated to the second division, and could not get past the group stages of the Malaysia Cup.

[13] In the 2002 season, Sabah was lining up players of calibre such as Zainizam Marjan, Khairul Azman Mohamed and Josiah Seton, finishing third in the league and again managed to get through to the final of Malaysia Cup by beating Selangor Public Bank and Perak.

[16] After 6 years in the 2nd tier MPL, Australian Gary Phillips was able to guide Sabah to promotion in 2010 – his first season in charge.

Sabah started their 2013 season back in the MPL as their main defenders Ronny Harun and Mafry Balang left and Rozaimi Abdul Rahman was loaned out to Harimau Muda A.

2013 season was led by Northern Irishman David McCreery and they end up in 5th place, but lost the Malaysia Cup play-off 0–4 to Negeri Sembilan at Shah Alam Stadium.

The year 2014 saw a major changes in the team's sponsorship by which local brand Carino was signed as their kit supplier and Ararat Sports plus BSA as their sponsor.

Sabah FA successfully signed twice African Player of The Year El Hadji Diouf and his compatriot Abdoulaye Faye, followed by Irish-born Libyan footballer, Éamon Zayed and Singaporean Fazrul Nawaz.

[24][25] Fazrul was replaced by Joel Chianese during the mid-season transfer window, and O'Callaghan by Brisbane Roar ex-coach Mike Mulvey in February 2015.

TC Goh, Mulvey and big name players such as Diouf, Zayed, Faye, Chianese and Rozaimi Abdul Rahman left at the end of the season due to no contract renewal.

[30] Following much efforts and various reorganisation made on the team, Sabah FA was crowned as the champion of the 2019 Malaysia Premier League for the first time since they last lifted the old first division title back in 1996.

[31] Having early secured various imports such as Brazilian Luiz Júnior, South Korean Park Tae-soo and Serbian Luka Milunović, Aguinaldo da Veiga, Ahmet Ataýew, Rodoljub Paunović and various local talents, the team was able to win 13 from a total of 19 matches, qualifying for the 2020 Malaysia Super League.

[36] Sabah finished in third place of the 2022 Malaysia Super League, which saw them returning to the continental club competition since 1995–96 and making their debut in the 2023–24 AFC Cup in the group H with Haiphong, Hougang United and PSM Makassar.

During the time, Sabah Football Club Sdn Bhd in its statement informed that the logo was created by an individual named Firzaruddin Zainal Abiddin.