As a law graduate, Pendarovski first worked as a trainee in a law office in Skopje, but later left and got a job at the Ministry of Internal Affairs, where he worked as a security analyst. In 1998, he was appointed head of the Ministry of Internal Affairs' Analysis and Research Administration and a spokesman for the ministry, in the capacity of Deputy Minister of Public Relations. He was a spokesman for the Ministry of Internal Affairs during the country's 2001 armed conflict.