Hrayr Mkoyan spent his youth career at Shirak Gyumri. He debuted for the first team at 18 years of age. In 2007, Mkoyan attracted breeders from Ararat Yerevan. For two seasons at the Yerevan team, Hrayr spent 47 meetings. Normal performance for the club prevented a permanent objective and subjective pressure on Ararat.[2]
Ulisses
In 2009, Mkoyan moved on loan to the capital club Ulisses Yerevan, with whom he won third place in the 2009 Armenian Premier League. However, after the lease agreement, Hrayr left Ulisses and signed a two-year contract with Mika Yerevan.[3]
On 12 January 2012, Mkoyan signed an agreement with the semi-annual club Spartak Nalchik. According to the agreement, if the Spartak will retain a place in the Russian Premier League, the contract will be extended for two years. Otherwise Hrayr leave the club in the status of a free agent.[5] Spartak took the last place in the First Division, and fell to the Russian National Football League, and Mkoyan became a free agent.
Shirak
In June, it was reported Mkoyan return to his native club Shirak Gyumri. Mkoyan himself did not refuse such an opportunity, if any. The parties were clearly set to work, and in the middle of the month the contract flock signature of both parties. Mkoyan officially returned to the location of the club where his career began, and the club returned to the existing experienced players to participate not only in the domestic competition, but also in European competition. The agreement is designed for six months.[6]
Loan to Dynamo
On 9 February 2013, Mkoyan tried out for Czech club Dynamo České Budějovice.[7] He joined the club two days later. According to head coach Miroslav Soukup, "Mkoyan made a good impression in a short time, and I think he will make our team stronger." A contract valid until the end of next season was signed.[8]
Esteghlal
On 16 June 2014, Mkoyan joined Iran Pro League club Esteghlal. He signed a two-year contract with the club.
Shirak
On 30 January 2018, Mkoyan returned to his native club FC Shirak, signing a six-month contract.
Alashkert
After starting the 2018/19 season with FC Ararat-Armenia, Mkoyan signed a one-year contract with FC Alashkert on 28 August 2018.[9]