When the two clubs joined to form AEP, APOP was in First Division, and managed to remain there, and Evagoras was in the Second division without managing to achieve promotion. Since APOP was in the First Division, the newly formed club of Paphos began its history from the First. They club remained in the first division until 2005, but soon had the luck of APOP and Evagoras when the team was for first time relegated to the Second Division. However, despite the fact that the team for the season 2005/06 was playing in the Second Division, on April 2006 they had their greatest success as a club since the team qualified for first time for the semi finals of Cypriot Cup (APOP reached the semi finals twice) by eliminating Olympiakos Nicosia. In the semi finals of the Cup they faced AEK Larnaca and despite the fact that Paphos was not beaten in none of the matches against AEK, they were eliminated with scores 1–1 at home and 0–0 away. The same season, AEP won the Second Division Championship and was promoted back to First division but after a very bad season were again relegated. The club had not justified the dreams of the people of Paphos of having a better team than APOP and Evagoras and to have a worthy team which will be permanent in the First Division.