The 1999–2000 Harty Cup was the 80th staging of the Harty Cup since its establishment by the Munster Council of Gaelic Athletic Association in 1918.

St Flannan's College were the defending champions.

[2] The final was played on 12 March 2000 at MacDonagh Park in Nenagh, between St Flannan's College and Our Lady's Secondary School, in what was their first ever meeting in the final.

St Flannan's College won the match by 3–14 to 3–08 to claim their 19th championship title overall and a third title in succession.

[3][4] Nenagh CBS's Niall McGrath was the top scorer with 3-28.