The 1999 Chatham Cup was the 72nd annual nationwide knockout football competition in New Zealand.
Up to the last 16 of the competition, the cup was run in three regions (northern, central, and southern), with an open draw from the quarter-finals on. In all, 132 teams took part in the competition. Note: Different sources give different numberings for the rounds of the competition. Some record five rounds prior to the quarter-finals; others note a preliminary round followed by four rounds proper.
The Jack Batty Memorial Cup is awarded to the player adjudged to have made to most positive impact in the Chatham Cup final. The winner of the 1999 Jack Batty Memorial Cup was Aaron Burgess of Dunedin Technical.