The origins of the Botanic Gardens date as far back as 1371, when King Wickramabahu III ascended the throne and kept court at Peradeniya near the Mahaweli river. The Botanical Gardens at Peradeniya was formally established in 1843 with plants brought from Kew Garden, Slave Island, Colombo and the Kalutara Garden in Kalutara. The Royal Botanic Gardens, Peradeniya, was further expanded under superintendent George Gardner in 1844.

As well as a magnificent Avenue of Palms, one tree within the Gardens with a particularly significant history is the Cannonball Tree, planted by the British monarchs King George V and Queen Mary in 1901. This unusual tree is bent with its fruits, which look like cannonballs.

During the Second World War, the Botanical Garden was used by Lord Louis Mountbatten, the supreme commander of the allied forces in the South Asia, as the headquarters of the South East Asia Command.