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The 1999 Cork Junior A Hurling Championship was the 102nd staging of the Cork Junior A Hurling Championship since its establishment by the Cork County Board. The championship began on 3 October 1999 and ended on 21 November 1999.
On 21 November 1999, Bandon won the championship following an 0–11 to 1–07 defeat of Courcey Rovers in the final at Páirc Uí Chaoimh.[1] This was their fourth championship title overall and their first title since 1971.
Bandon's James Nyhan was the championship's top scorer with 1-12.