The site of these botanic gardens was selected in 1866, replacing an earlier site near the mouth of the Hopkins River. The early development of the gardens owes much to Charles Scoborio, curator, and Government botanist Ferdinand von Mueller.
In 1877 Warrnambool Council commissioned William Guilfoyle, then Director of the Melbourne Botanic Gardens, to design an appropriate layout. His vision of sweeping lawns and long curving paths where the viewer can gaze into the distance, was implemented by successive curators, and remains intact.
The Warrnambool Botanic Gardens Conservation and Development Plan was carried out in 1995 with the assistance of funds made available by the Commonwealth of Australia under the National Estate Grants Program.