The 1998–99 Harty Cup was the 79th staging of the Harty Cup since its establishment in hurling by the Munster Council of Gaelic Athletic Association in 1918.

[1] The competition ran from 14 October 1998 to 7 March 1999.

St Flannan's College successfully defended its title[2] in the Harty Cup final on 7 March 1999 at Páirc Caoimhín Ó Luing in Feenagh, against St Finbarr's College, 1–14 to 1–08, in what was their fourth successive meeting in a final overall and a first meeting in 27 years for their 18th successive Harty Cup title overall and a consecutive title since the previous season.

[3]