Akademik debuted in A PFG in 1949 and would quickly establish themselves as a top-flight team in Bulgarian football from then on. The team became one of the top Bulgarian teams in the 1950s and 1970s, especially in the domestic and European Cup competitions, having been crowned Balkans Cup champions.
Akademik was founded in the 1947, by Sofia University (the oldest higher education institution in Bulgaria, founded on 1 October 1888) students as a football club. A two years later, Akademik were promoted for the first time to Bulgarian A PFG. The 1950 season in the domestic league was very successful for the team, which finished 3rd in the top division. In the next campaign Akademik finished fourth and reached the final of Bulgarian Cup, losing 0-1 to CSKA Sofia. In 1952 the club's form dropped, however, and they were relegated to B PFG finishing before the last Spartak Varna. In 1963-64 season they won a second promotion to the top division by winning the B PFG. However, the next year they were relegated again.
The third promotion to A PFG in 1969 marked the beginning of Akademik's golden age. From 1969 to 1979 they spent their longest ever period in the top division. In 1974 Akademik won first international throphy, beating Vardar Skopje 2-0 on aggregate in the final of Balkans Cup. In the 1975-76 season the team finished 3rd in the domestic league and qualified for first time in UEFA Cup. At the European level Akademik made a memorable appearance in the second round against Italian giants A.C. Milan, winning 4:3 at home on 20 October 1976. Before reaching the second round of the football competition, the Students eliminated the Czech Slavia Prague respectively. In this period two players from Akademik have played for the Bulgarian national squad during at FIFA World Cup: Ivan Dimitrov in 1970 and Mladen Vasilev in 1974.
In the 1978-79 season Akademik won just six games in the campaign and were relegated. In the next season the team won promotion back to the top division, scoring 100 goals in the campaign. In 1981 the Students qualified for second time in UEFA Cup, where they lost 1-3 on aggregate in the first round against 1. FC Kaiserslautern. In the same 1981-82 season Akademik again relegated. From 1982 to 2010 they spent their longest ever period out of the top division.
After 28 years in the lowers divisions of Bulgarian football, in 2009-10 Akademik finished 2nd in B PFG and the club managed to participate in the play-off for promotion in the A PFG. On May 23, 2010, Akademik surprisingly won the play-off against Nesebar with a result of 2:1 and finally qualified again for the top division. However, Akademik were relegated from A PFG at the end of the 2010/2011 season after finishing in 15th place.