Karlen Mkrtchyan is a graduate the Armenian football club school Pyunik Yerevan.

[7] On 9 January 2015, Mkrtchyan signed a one-year contract with Kazakhstan Premier League side FC Tobol,[8] leaving the club on 22 April of the same year through mutual consent.

[12] On 17 August 2017, Mkrtchyan signed a one-year contract with his former club Pyunik of the Armenian Premier League.

[19] Mkrtchyan scored his first goal for the Armenia national team on 14 November 2012 in a home friendly match against Lithuania at the 50th minute.

[20] Following the 14 November 2012 Armenian national game, in which Mkrtchyan scored his first goal for the team, he headed back to Donetsk together with his wife and got married.