Arajuuri and Brøndby's 2017–18 season began with the qualifying matches of the Europa League, where they, among others, faced Finnish Veikkausliiga side Vaasan Palloseura. However, Brøndby were knocked out before reaching the group stage. Arajuuri consolidated his place in Brøndby's starting line-up and made a total of 28 Superliga matches as well as two Europa League qualifying matches. He scored his first goal in the Superliga on 3 December 2017 in a 1–3 away win over SønderjyskE. The team led the Superliga during large parts of the season, but finished second, as in the previous season, when FC Midtjylland won the championship. Brøndby again made it to the Europa League qualifiers, and the team went on to win the Danish Cup by beating Silkeborg IF in the final.