The team has won the Malaysia FA Cup (1995) and Premier League in 1996. In 1995, the team also advanced to the second round of the Asian Cup Winners' Cup after beating An Giang of V-League by 3–1 on aggregate, only to crashing out later to Bellmare Hiratsuka of J-League by 1–7 on aggregate.
From the 1950s until 1963, Sabah competed as North Borneo football team in the Borneo Cup together with Sarawak football team and Brunei national football team. Following the formation of the Federation of Malaysia, the North Borneo Football Association (NBFA) changed its name to Sabah Football Association (Sabah FA). Sabah qualify into the Malaysia Cup for the first time in 1977 and enter the competition in 1978.
Sabah was a well known team during the Malaysian football amateur and semi-pro era as state team produced many quality players namely the trio of James Wong, Hassan Sani and Peter Rajah. These players during their time led Sabah to become one of Malaysian football's most feared teams during the 80's. One fine example was during the 1979 Malaysian League where Sabah started slowly. After a run of 8 matches, they stood with 3 wins, 2 draws and 3 losses but, during the later stages they stepped up a gear or five by winning all their remaining 8 matches with most of them by huge margins, including an incredible 8–0 thrashing of Sarawak, 11–0 hammering of Perak and the 6–1 beating of Terengganu. At the end of the season, Sabah finished as runners-up behind Singapore and became the highest scoring team with 49 goals in 12 games, which is an average of 3 goals per game. In 1991, Sabah striker Matlan Marjan became the first Malaysia to score a double against England in 'A' international matches on 12 June 1991.
When professional football was introduced by Football Association of Malaysia (FAM), Sabah also made a reputation of being one of the Malaysian League's most competitive teams. Quality professional 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 the then Malaysian national team coach Claude Le Roy. The positive results gained from the beginning of professional era however was cut short by the match fixing scandal that rocked Malaysian football in 1994. The scandal almost destroyed Sabah and Malaysian football in general. Matlan was the one of several players found guilty for being involved in the scandal. As a punishment for their involvement in match fixing, he and the other players were banned for life by FIFA from being involved in football and banished from the state of Sabah by the state government under the Restricted Residence Act. After the scandal, Sabah began its rebuilding process to regain their reputation in Malaysian football. Sabah won their first professional trophy, the Malaysia FA Cup in 1995. In the 1996 season, Sabah won their first league title and went through to the final of the Malaysia Cup for the first time but were beatened by Selangor on penalties. The 2000 season could be considered as Sabah's worst since joining the Malaysian professional league. They were relegated to the second division and could not get past the group stages of the Malaysia Cup. However, Sabah quickly regained its performance in the 2001 season where they finished as runners-up behind Johor FC. In the 2002 season, Sabah lining up players of calibre such as Zainizam Marjan, Khairul Azman Mohamed and foreign striker Josiah Seton, finished third in the league and again managed to get through to the final of Malaysia Cup by beating Selangor Public Bank and Perak. Sabah however finished as runners-up yet again by losing to the same team that beat them in 1996 final, Selangor. This time, Sabah lost by 'golden goal' scored by Mohd Amri Yahyah. In 2003, Sabah again finished third in Liga Premier One. Sabah again reached the final of Malaysia Cup. This time they lost to club-side Selangor MPPJ by 0–3, with hat-trick from Juan Manuel Arostegui.
When the Malaysia Super League (MSL) was introduced in 2004, Sabah struggled to be competitive against other teams in the top league. Sabah only managed to stay in Super League for two seasons as they were relegated to Malaysia Premier League (MPL) for the 2005/06 season. After the relegation to 2nd tier league, Sabah continued to struggle for promotion to get back into the top division. They lost to Pahang in the 2006/07 season play-off for a place in 2007/08 Malaysia Super League. After 6 years playing in the 2nd tier MPL, Australian coach Gary Phillips was able to guide Sabah to promotion in 2010 – his first season in charge. After poor results which have affected Sabah's performance in the 2011 league and also the cup, Gary Phillips was replaced by Justin Ganai to save Sabah from relegation zone. Justin improved Sabah performance in 2011 Malaysia Cup where the team reached the quarterfinals. He was retained as head coach for the 2012 MSL season but step down as the league game were 2 games left. Sabah also relegated back to MPL after lose to Kedah in play-off match by which Pahang (was MPL side) won the play-off. Salt was added to the wound as the relegation was followed by them failing to qualify to the group stage of the 2012 Malaysia Cup. Sabah started their 2013 season back in MPL as their main defenders, Sipitang duo Ronny Harun and Mafry Balang left for Borneo rival Sarawak and Bongawan young striker 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 still available for Malaysia Cup play-off by which they lose heavily 0–4 to Negeri Sembilan at Shah Alam Stadium. McCreery left at the end of the season with disappointment. 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 sponsors. During this season, Sabah ex-player and also a legend in 90's, Milomir Šešlija become their head coach replacing McCreery in the hot seat. National striker, Rozaimi and winger/midfielder Maxsius Musa also returned after their loan to Harimau Muda A and Harimau Muda B respectively finished. But to no avail, they finished 8th out of 12 in the MPL, missed the Malaysia Cup group stage for third consecutive seasons and also kicked out from FA Cup in the early stage. This was worse than the 2013 season. Milomir's contract was not renewed at the end of the season.