FC Panjsher was founded in 1973 under the name "Trud" during Soviet times.
In 1997, Panjsher made their debut in the Tajik League, the top division in Tajikistan, under the name "SKA-Panjsher".
From 1998 to 2003 the club used the name "Panjsher", during which they were runners up to Regar-TadAZ in 2001. Panjsher were relegated from the Tajik League in 2003 and went on to play in the Tajikistan First League in 2005, 2009 and 2011. In 2012 Panjsher won the Tajikistan First League Dushanbe division, earning promotion back to the Tajik League for 2013. During the 2013 season Panjsher only played 5 matches before withdrawing form the Championship, returning to the First League for the 2014 season.