Trajkovski became active in politics following the Republic of Macedonia's declaration of independence from Yugoslavia in November 1991, when he joined the VMRO-DPMNE party. He played an important role in developing the party's relations with other European political parties and was appointed Chairman of the party's Foreign Relations Commission. In 1997, he became the Chief of Staff of the Mayor of Kisela Voda, a municipality in Skopje. He was appointed Deputy Minister of Foreign Affairs on 21 December 1998 but served in this post for less than a year.