Trajkovski began his career with FK Cementarnica 55. In May 2010, he joined Chelsea in a trial, scoring the winning goal against Botafogo at the U-19 Copa Amsterdam tournament which guaranteed Chelsea a place in the semi-finals.[2]
After a few years with Cementarnica Skopje, he signed for Inter Zaprešić in the summer of 2010.[3] Good performances in the second half of the season attracted the interest of Dinamo Zagreb,[4][5] but Trajkovski said that he was not interested in a possible move. At the end of the season, R.S.C. Anderlecht was interested in buying Trajkovski, but their offer of a €500,000 transfer fee was rejected.[5] He joined the Belgian club Zulte Waregem for the new 2011–12 season after their offer of €1.1m was accepted by Inter Zaprešić.[5][6]
In the summer of 2015, he moved to Italian Serie A club Palermo, signing a five-year contract.[7] In the same year, he was named "Macedonian footballer of the year".[8] Following Palermo's exclusion from the Serie B, he was released together with all other players in July 2019.
On 7 August 2019, Trajkovski agreed to a four-year contract with La Liga newcomers RCD Mallorca.[9] After two seasons at Mallorca, Trajkovski was loaned out to Danish Superliga club AaB on 31 August 2021, for the rest of the season.[10]