The club was founded as Pirin in 2002. In their second season, they were promoted to South-Western V Group (third tier) as champions of the Regional Group - Blagoevgrad.
In 2010, Ivan Stoychev had been appointed as a manager of Pirin 2002. In 2011–12 season, the club won promotion for the B Group for first time in the club's history.
On 24 June 2016 Pirin merged into PFC Septemvri Sofia. In August 2016 the restored club merged with Malesh Mikrevo and from the new season 2016/17 Pirin will compete in the new Third Southwestern League, the third division of Bulgarian football.