In accordance with a pre-agreement made in July 2016, Arajuuri joined fellow Finn Teemu Pukki at Danish Superliga club Brøndby IF in January 2017. Arajuuri made his debut in the Superliga on 12 March 2017 in an away match against AC Horsens. He made eight matches during the spring season 2016–17, six of them in the starting line-up. Brøndby finished second in the Danish league after FC Copenhagen, who took the championship. Brøndby qualified for next season's UEFA Europa League qualifiers, and the team also made it to the Danish Cup final, which was lost to Copenhagen.