It was established on 23 February (the traditional Defender of the Fatherland Day holiday) in the year 2000.

On Shushi Liberation Day in 2013, a newly erected building for the union was opened on Renaissance Square in Stepanakert (Khankendi).

The union had a youth wing called Hayrenyats Pashtpan (Motherland Defender), which was established in April 2006.

In 2007, personnel of the union took part in the Liberation Day military parade for the first time.

In early March 2024, Azerbaijani authorities demolished the Artsakh Freedom Fighters Union building.