The club currently competes in the Gamma Ethniki, the third tier of the Greek football league system.

Despite being founded in 1982, Paleochora made its official Chania FCA League debut during the 1990−91 season, when they instantly won the C regional Division title and earned promotion to the B Division.

[1] Afterwards, they played for three seasons in the B Division, achieving promotion to the Chania FCA A Division during the 1993-94 season, after finishing 3rd in the B League and winning the promotion play-off match vs. Ikaros Tavronitis.

[1] Paleochora featured in 11 consecutive editions of the Chania FCA A Division, achieving its best finish in 2002 (5th), the same year it reached the Chania FCA Cup Final.

[1] In 2017, Paleochora won its first ever Chania FCA A Division championship, managing instant promotion to the Gamma Ethniki, the third tier of the Greek football league system.