After returning from China in 1998, during Seyed Kamal Kharazi's term as the minister, Mirfakhar was appointed Director General for Administrative Affairs and with the minister's recommendation, he worked on the revival and implementation of the Internal Regulation of the Ministry of Foreign Affairs and brought some other administrative reforms. Later, in 2002, he moved to Dublin as the Ambassador of the Islamic Republic of Iran in the Republic of Ireland. After completing his mission and returning from Republic of Ireland in 2005, he served as Senior Expert in Political Studies.