In 2005, Harutyunyan co-founded the Free Motherland party, which took part in the 2005 parliamentary election, winning 10 out of 33 seats in the National Assembly of Artsakh.

[9] He resigned from the position in June 2018 after four days of protests in Stepanakert sparked by the beating of two civilians by Artsakh's security forces.

[13][14] During the ceremony, which was held in Shusha instead of Stepanakert (a decision which angered the authorities in Baku),[15] he described Artsakh and Armenia as "inseparable parts of a united national homeland".

[17] During the 2020 Nagorno-Karabakh conflict, the Ministry of Defence of Azerbaijan claimed that the Azerbaijani Army had severely wounded Harutyunyan, who had visited the front that morning.

[25] On 9 November, Harutyunyan gave his consent for Nikol Pashinyan to sign the 2020 Nagorno-Karabakh ceasefire agreement between Armenia, Azerbaijan and Russia.

[26] Harutyunyan defended the decision to accept the ceasefire agreement, stating that the Armenian side "would have lost all of Artsakh" if the war had not been stopped.

[29] On 1 December 2020, Harutyunyan announced that a national unity government would be formed and a number of cabinet officials would be replaced, pending snap elections.

[32][33] On 4 November 2022, Harutyunyan appointed Ruben Vardanyan, a Russian Armenian billionaire who had recently moved to Artsakh, to the position of state minister with "broad powers".

[35] In December 2022, Azerbaijan began a blockade of Nagorno-Karabakh by blocking the Lachin corridor, the sole road linking Artsakh to Armenia and the rest of the world, precipitating shortages of essential supplies such as food, medicine and fuel.

[39] Harutyunyan did not give details about the reasons for the dismissal, but claimed that it was in Artsakh's best interests and denied that it was in response to Azerbaijan's demands for Vardanyan's departure.

He called on Russia to carry out its obligations according to the 2020 ceasefire agreement and asked the Armenian government not to recognize Artsakh as a part of Azerbaijan.

He also stated that the defeat in the 2020 war and subsequent events had "significantly reduced the trust [among the inhabitants of Artsakh] in the authorities, especially the President," which was limiting the effectiveness of the government.

[3][4] Previously on 1 October, an arrest warrant had been issued for him by Azerbaijani Prosecutor-General Kamran Aliyev, for Harutyunyan's role in ordering the 2020 Ganja missile attacks.