The club was founded in 2008, after the union of the two clubs from Blagoevgrad – Pirin and PFC Pirin Blagoevgrad. The new club is the historical successor of the original and traditional club records of the former FC Pirin which was founded in 1922.
The club's home ground is the Hristo Botev Stadium in Blagoevgrad with a seating capacity of 11,000, which was expanded after the winter break of the 2010–11 season by making completely new all-seater east stand.
On August 18, 2006, after failing to arrange some debts and signals of corruption, Pirin was thrown out of the A PFG, the team's results for the season were annulled, and the club was demoted to play in the Bulgarian South-West V AFG. However, after two years, Pirin won the South-West V AFG and the club returned for the upcoming season of the Western B PFG.
In December 2008, Pirin, which played in the Western B PFG, merged with PFC Pirin Blagoevgrad, which played in A PFG. The new club was named FC Pirin Blagoevgrad and is officially the rightful holder of the club records of the former Pirin, which has played more than 20 seasons in the top flight. FC Pirin's Western B PFG place was taken by FC Bansko. Then, Nikolay Galchev was appointed manager of the club Petar Mihtarski. A few months later, the successes came nearby and Pirin qualified for the final of the Bulgarian Cup, beating CSKA Sofia and Levski Sofia). However, in the final, they suffered a 3–0 defeat against Litex Lovech.
In the foremath of the 2011–12 season, Pirin Blagoevgrad did not receive a professional license to compete in A PFG. However, due to their financial struggles they did not participate in the South-West V AFG either.