Hayk Hovhannisyan worked at Ararat from 2012 to 2014, being the translator of the first team.
In 2014, he had his first coaching job, working in the "Perugia" children's and youth system. Then he worked in "Pyunik" as an assistant physical coach. In the 2018/19 season, Hovhannisyan was the head coach of FC Yerevan. After Yerevan, Hayk Hovhannisyan was the technical advisor of West Armenia FC, and from July 2021 to January 2022 he worked at the Lithuanian "Mariampole City" academy as the head coach of the senior team, coordinator of the coaching department.
In January 2022, Hayk Hovhannisyan was included in the FC Ararat coaching staff as an assistant to head coach Edgar Torosyan.