Founded in 1992 as Homenetmen Yerevan, the club won the first Armenian Premier League competition held in 1992 (shared with Shirak). In 1995, Homenetmen Yerevan was renamed FC Pyunik (Armenian for "Phoenix").
The new era of Pyunik began in 2001, when they absorbed the newly-promoted club FC Armenicum and automatically gained position in the Armenian Premier League without playing a single game in the lower leagues. The new owner of the club Ruben Hayrapetyan, took serious approach to develop the team bringing star players from other Armenian clubs. Pyunik had significantly improved after the arrival of foreign players from Mali, Cameroon, Argentina and later from Romania. Thus, Pyunik won the Armenian Premier League title the same year and the Armenian Cup in 2002. Later, for the first time in independent Armenian club history an Armenian club advanced to the second round in the Champions League. Afterwards, the club won the Armenian Premier League title ten times in a row.
Between 1992 and 1999, the club used the Hrazdan Stadium as a home ground. After the renovation of the Republican Stadium in 1999, the club moved there and used it regularly as a home ground until 2013. Howevere, FC Pyunik were forced to play their home games at their own Pyunik Stadium of 800 seats in 2008, due to the large-scale renovation works at the Republican Stadium.
Pyunik's main two rivals are Ararat and Banants, however, the rivalry with Ararat is a lot more fierce than that of Banants. The reason for that is because Ararat is known to be the most loved club of Yerevan because of its Soviet accomplishments, and Banants was originally based in the region of Kotayk, and was only moved to Yerevan in 2001. Another category Banants and Pyunik compete is their youth academies, which are considered to be the two best academies in the country.