Born in Skopje into a family originally from Udovo, Gjoko Zajkov was playing in Macedonia for the youth team of Rabotnichki, until the summer in 2012 when he made his first appearance for the senior team of the club, competing in the Macedonian First League.

On 23 June 2014 he left Macedonia for the French club Stade Rennais F.C., with whom he signed a three-year contract.

[1] After his first season in France, where he spent the majority of the time playing for the youth team of Rennais only, in the summer of 2015 he was loaned for one year to Charleroi in Belgium.

After being released from Charleroi, Zajkov signed a one-year deal with Levski Sofia in August 2021.

He made his senior debut for Macedonia in a June 2016 friendly match against Iran and has, as of May 2020, earned a total of 12 caps, scoring no goals.