The 1998–99 Cypriot Cup was the 57th edition of the Cypriot Cup. A total of 50 clubs entered the competition. It began on 14 November 1998 with the preliminary round and concluded on 8 May 1999 with the final that was held at Tsirion Stadium. APOEL won their 17th Cypriot Cup trophy after beating Anorthosis 2–0 in the final.