Arajuuri continued in Brøndby's starting line-up as a player in the 2018–19 season. Brøndby once again played in the Europa League qualifiers, where they were eventually knocked out by Genk before reaching the group stage. Arajuuri played a total of 26 league matches during the season, as well as three Europa League qualifiers. Brøndby finished fourth in the Superliga and reached the European League qualifiers after play-offs. Again, Brøndby reached the Danish Cup final at the end of the season, but this time lost to Midtjylland.