President Trajkovski and eight other people, including three members of his cabinet, died in a plane crash in Bosnia and Herzegovina on 26 February 2004.

When the plane crash happened, Pendarovski was in Dublin as a representative of President Trajkovski in the state delegation that was due to submit the country's application for EU membership that day, which was subsequently postponed.

In 2005, he returned to the presidential cabinet, this time as an advisor to President Branko Crvenkovski on national security and later on foreign policy.

[15] During the COVID-19 pandemic, Pendarovski introduced the nation's first ever state of emergency to contain the coronavirus, a move that paved the way for a 2020 parliamentary election.

[16] In February 2022, Pendarovski was seen walking with Embla Ademi, an 11-year-old girl with Down syndrome, to her elementary school in Gostivar after he heard she was being bullied.