The 1999 All-Ireland Junior Hurling Championship was the 69th staging of the All-Ireland Junior Championship, the Gaelic Athletic Association's second tier Gaelic football championship.
Tipperary entered the championship as the defending champions, however, they were beaten by Kerry in the Munster quarter-final.
The All-Ireland final was played on 7 August 1999 at O'Moore Park in Portlaoise, between Waterford and Meath, in what was their first ever meeting in the final. Waterford won the match by 2âÂÂ12 to 2âÂÂ11 to claim their first ever championship title.