On 14 January 2007, in the reverse fixture of their earlier draw, Ayia Napa beat Omonia Nicosia 2–1, arguably the most impressive result in the clubs' history.

Another big achievement of Ayia Napa FC is the qualification to the cup's quarter-finals group stage in the 2007–08 season while the team was in the Cypriot Second Division.

The club finished third in the group stages with wins against APOEL and Aris Limassol.

The UEFA European Under-19 Football Championship was hosted in Cyprus in 1998 and the UEFA European Under-16 Football Championship in 1992 and the Ayia Napa Stadium was used for two matches of Republic of Ireland in each competition;[1] on 19 June 1998, their 5–2 victory against Croatia and four days later, their 3–0 Cyprus U-19 national team and qualified to the final where they went on to win the trophy.

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