The 1999 AFL reserves season was the 80th and final season of the AFL reserve grade competition, the Australian rules football competition operating as the second-tier competition to the Australian Football League (AFL).

Essendon won their 8th reserves premiership, defeating St Kilda by 52 points in the grand final on 25 September.

Following the end of the season, the AFL reserves was disbanded and merged into the Victorian Football League (VFL).^[1]

From 1995 until 1999, the Victorian State Football League operated its two open-age competitions – the VFA/VFL and the Victorian AFL reserves competition – separately; however, its intention had always been to merge the two, and this took place at the end of the season, after the agreement of the AFL clubs. Under the administration's new name Football Victoria (later AFL Victoria), the two competitions were merged into a single competition still known as the Victorian Football League.^[3]

Under the new arrangement, three Victorian AFL clubs opted to end their reserves teams and enter into affiliations with existing VFL clubs:^[4]

• Hawthorn affiliated with Box Hill
• Western Bulldogs affiliated with Werribee and Williamstown
• Melbourne affiliated with Sandringham

Additionally, Sydney entered a partial affiliation with Port Melbourne, the club with which it had shared a zone when it was based in South Melbourne. No more than six of Sydney's reserves players played for Port Melbourne; the rest played for a dedicated Sydney reserves team in the Sydney AFL competition.