The Kumpula Manor was in the 19th century one of the largest and best-managed estates in the Helsinki area. The estate, covering more than four square kilometers, was established at the site of the village called Gumtäckt at the end of the 15th century. Over the centuries, Kumpula Manor had numerous owners. It did not remain within a single family from one generation to the next but instead passed frequently from noble owners to wealthy commoners, sometimes as payment for debts and sometimes pledged as collateral.

The manor stayed in private ownership until the end of the 19th century. The last private owner was Baron Herman Standertskjöld-Nordenstam. During his time, the estate shrank as land was sold for residential construction.

The city of Helsinki purchased the land in 1893, after which the area served as a dairy producer until 1905. Following that, the manor housed a venereal disease hospital, which remained in operation until 1960. A primary school later began in the manor but was closed in 1977 as part of the comprehensive school reform.

Since then, the manor has been under the administration of the University of Helsinki. The botanical garden began construction in the 1980s and was opened to the public in 2009.