Their biggest achievement in European football was reaching the 2002–03 UEFA Women's Cup final where they ultimately lost 1–7 on aggregate to Umeå IK.

[1][2] The next try at a European Cup came in 2009–10 with the newly created UEFA Women's Champions League.

In the 2016–17 season they reached their best result since the final in 2003, when they made it to the quarter-finals which they lost 0–2 on aggregate to Manchester City.

All results (away, home and aggregate) list Fortuna Hjørring's goal tally first.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.