Hovhannisyan was born in Yerevan. In 1978, he graduated from the Moscow Pedagogical Institute with degrees in history and archaeology. After serving in the Soviet Army from 1978 to 1980, he was a research assistant. From 1990 to 1992, he participated in the Nagorno-Karabakh War.
He was a member of the ARF Central Committee from 1990 to 1992 and a member of the ARF Bureau from 1992 to 1995. He was jailed from 1995 to 1998. Afterwards, he was an advisor to Robert Kocharyan, the President of Armenia, as well as head of the Commission on Issues of Local Self-Government, from 1998 to 1999. He has been a deputy in the National Assembly since 1999; he was re-elected in May 2003 and May 2007, and on June 7 2007 he was elected as the Vice-President of the National Assembly.
In the presidential election held on February 19 2008, Hovhannisyan, running as the ARF candidate, won 6.2% of the vote. Shortly after the election, on February 21, Hovhannisyan resigned from his position as Vice-President of the National Assembly due to his disapproval of the handling of the election.