Trajkovski was born into a Methodist family. His father, Kiro, who died in September 2008, was a landworker who had served in the Bulgarian Army and had been imprisoned for two years for feeding prisoners of war. Trajkovski graduated in 1980 with a degree in law from the Ss. Cyril and Methodius University in Skopje. He subsequently specialized in commercial and employment law and made several visits to the United States, where he studied theology to become a Methodist lay minister.