Bali Botanic Garden was established on 15 July 1959. The Garden was first known as the Eka Karya Botanic Garden, where "Eka" means first while "Karya" means creation in the Balinese language, referring to the garden's status as the first Indonesian botanic garden to be established after independence.

It was originally intended that The Bali Botanic Garden specialise in the cultivation of conifer plants (non-flowering seed plants or Gymnosperms) and as a place for recreation. The garden accommodates scientific, cultural and recreational activities for visitors.

Development of the garden stopped in 1965 due to political instability before being reopened on 30 April 1975. When the garden became operational once again, its area was expanded to 129 hectares. It also added a new focus: the ex-situ conservation of plants from the mountainous regions of Eastern Indonesia.
In 2001, the land area of the Garden was expanded again to its current size of 157.5 hectares.