The garden is located in the city center and adjoin the presidential palace compound of Istana Bogor.

Founded in 1817 by the order of the government of the Dutch East Indies, the garden thrived under the leadership of many renowned botanists including Johannes Elias Teijsmann, Rudolph Herman Christiaan Carel Scheffer, and Melchior Treub.

Since its foundation, the Bogor botanical garden has served as a major research center for agriculture and horticulture.

[1][citation needed] The area that is now Bogor Botanical Gardens was part of the samida (man-made forest) that was established at least around the era when Sri Baduga Maharaja (Prabu Siliwangi, 1474–1513) ruled the Sunda Kingdom, as written in the Batutulis inscription.

After the successful British invasion of Java in 1811, Stamford Raffles was appointed as the island's lieutenant-governor, and he took Buitenzorg Palace as his residence.

Among those on board was the German-born botanist Caspar Georg Carl Reinwardt, who was appointed as head of agriculture, arts and science of the colony.

A year later he proposed the establishment of a botanical garden, a move which was supported by Governor-General Van der Capellen.

The garden was officially founded on May 18, 1817, next to the palace grounds through a collaboration with two botanists, William Kent from Holland and James Hooper from Kew.

Much of his taxonomic work was catalogued by his successor Carl Ludwig Blume in 1823, who recorded 914 plants in the garden.

Seven years later Justus Carl Hasskarl was appointed as his assistant curator and convinced the director to re-arrange the plantings in the garden by taxonomic families.

The garden also played major role in the introduction of Cinchona trees to Java in 1854, which would ultimately make the island the largest producer of quinine bark for malaria treatment.

[3][5] The growth in economy and the effective directorship of Rudolph Scheffer and Melchior Treub, fueled the maturation of the garden as a leading regional center for biological study.

[10] The garden enjoyed wide international attention and was regularly visited by botanists and biologists from various countries to conduct research.

Part of the new section was arranged in similar manner to the main garden, with the rest laid out as large lawns, avenues, ponds, teahouses and glasshouses for orchids.

Two Japanese botanists were appointed in charge of the botanic garden, Professor Takenoshin Nakai (中井猛之進) as director and Kanehira (兼平) as head of the herbarium.

He promoted scientific biological research at the garden, which would ultimately bring various benefits to pharmaceutical industries and agriculture development in Indonesia.

The main gate is located in the south and is where most of the garden facilities are concentrated, such as ticket purchasing booth, Treub's laboratory, Nusa Indah Guesthouse, plant/souvenir shops, the library and the conservation building.

The precinct east of Ciliwung was laid out in 1927 with facilities as the mosque, cafes, Herbarium, orchid section and Wisma Tamu guesthouse, near Astrid's avenue.

Nearby the Bogor palace's bamboo collection section there is a small cemetery with Dutch tombstones.

[21] Situated behind the seed bank of the garden, an area devoted to Araceae species of flora was built in 2010.

Approximately 10 trees with a height of more than 2 m have been planted in this garden area, functioning as a protection from direct sun exposure.

The laboratory functions as a research facility for Puslitbang biologi's konservasi ex Situ (Conservation of species outside their original habitat).