The zoo was opened in 1928 by His Royal Highness Almarhum Sultan Sir Ibrahim Ibni Almarhum Sultan Sir Abu Bakar and named as the Kebun Binatang, which is Malay for Animal Garden, or zoo. At the time, the Johor Zoo was the first of its kind in Southeast Asia. On 1 April 1962, the zoo was handed over to Johor State Government and opened to the public that same year. The 12.5 acre Johor Zoo is located 1km from Johor Bahru City Centre and is the only zoo administered by a state government in Malaysia.
In 2016, the state government approved the relocation of the zoo from Johor Bahru to 20.23 hectares (50.0 acres) of land in Iskandar Puteri with a budget of MYR53 million.