The small hill of the Japanese Garden was built after World War II, from construction debris of the Zoo and buildings near-by. In the beginning it was the site of an open air theatre-stage, out of use for most part of the year, and occupying an otherwise too small an area. In it's place, the Japanese Garden was planned, together with a garden-library, though the latter functioned only for a few years. The decision of the Zoo to establish a Japanese Garden dates back to 1958. Following almost 10 years of preparations, the former stage-area was put under grass, the relief was formed, and paths restored. The first pine-trees and evergreens were presented to the Zoo in 1966 by the Silviculture /Forestry Research Institute. Later, seeds were donated from the Hokkaido Ohasi Botanical Garden, the Aritaki Arboretum and the Nippon Shinyaci Botanical Research Institute of Kyoto.
When the Garden first opened to the public, one could approach the lake by passing through the elevated area, situated right before the trees. The lake was fed by a gently flowing rivulet/stream/brook, which gradually widened , as it passed and trickled over and around a group of water-fall stones. With a closer look, one could noticed the characteristic "turtle stones", seemingly on their way to Horai Island, right in the middle of the lake. In 1998 a pavilion was built to house the National Bonsai Collection. The collection exhibited here includes the twenty valuable trees given as presents by the Japanese-Hungarian Friendship Society of Aichi Prefecture, as well as those presented by the University Bonsai Club of Hungary. Under the guidance of master Sugimura Fuimo, the Garden was renewed again in the year 2000. Plants were rejuvenated, some replaced and the Garden enriched with a new stone lantern (Isodoro), a basin for washing hands (chozobachi), a knocker to ward off game of the woods (Sisodoshi) as well as an observation hut. In the Spring of 2000 three unique, registered trees were received from Japan.