1998–99 Harty Cup

The 1998–99 Harty Cup was the 79th staging of the Harty Cup since its establishment by the Munster Council of Gaelic Athletic Association in 1918. The competition ran from 14 October 1999 to 7 March 1999.

St Flannan's College were the defending champions.

The Harty Cup final was played on 7 March 1999 at Páirc Caoimhín Ó Luing in Feenagh, between St Flannan's College and St Finbarr's College, in what was their fourth meeting in the final overall and a first meeting in 27 years. St Flannan's College won the match by 1–14 to 1–08 to claim their 18th Harty Cup title overall and a second title in succession.