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Rules for classification: 1. premiership points; 2. percentage; 3. points for Average score: 95.7 Source: AFL TablesEssendon finished one game clear on top of the ladder with 18 wins, and thus claimed its 15th minor premiership. The Kangaroos were second with 17 wins, trailed by the Brisbane Lions in third place with 16 wins, but with the best percentage of any team in the Eight. In fourth place were the Western Bulldogs who finished with 15 wins and a draw. The following three teams (West Coast, Carlton and Port Adelaide) finished with 12 wins each, separated by percentage. Sydney (with 11 wins) rounded out the Eight.
The 1999 finals series was probably best remembered by the preliminary final boilover, in which Carlton upset minor premier Essendon by one point at the MCG, which qualified them for an unexpected Grand Final appearance against the Kangaroos.
The 1999 AFL season would also be the last season which used the McIntyre system. It was replaced the following year with the AFL final eight system.