Hovhannisyan played for FC Pyunik before switching in July 2004 to Greek team Olympiacos.
[1] In January 2008, he moved on loan from Olympiacos to Greek Beta Ethniki club Agios Dimitrios.
In 2010, Zhora joined the now disbanded Russian club Saturn Moscow Oblast.
Soon afterward, he joined Lokomotiv Tashkent which was coached by his father Khoren Hovhannisyan.
[6] Hovhannisyan scored his first goal for Pakhtakor in a home 2–0 victory over Neftchi FK.