The academy was founded in 2010 by the Macedonian football player Goran Pandev, after whom the Academy was named.[1] As of 2014, Akademija Pandev has a senior team competing in the Macedonian senior leagues. In 2017, the senior team was promoted to the Macedonian First League for the first time in its history.[2]
In February 2018, the team moved to play their home games at Stadion Kukuš due to a disagreement over rent with FK Belasica.[3]