The idea of creating a permanent botanical station in the Khibiny Mountains was first proposed by geobotanist V. N. Sukachev after the 1920 expedition. However, in the early 1920s, there were no funds to realize this idea.

In 1930, thanks to the initiative of Academician A. E. Fersman, the Khibiny Mountain Station of the USSR Academy of Sciences "Tietta" was established, which later became the basis for the Kola Scientific Center. In the same year, a botanical team led by S. S. Ganeshin worked in the Khibiny, which included geobotanists A. A. Korchagin and M. V. Selyaninova-Korchagina, bryologist O. F. Gaaze, and lichenologist K. A. Rassadina. Ganeshin was tasked with organizing the Polar-Alpine Botanical Garden and studying the region's flora. However, on August 30, 1930, he died in the mountains due to fog and a snowstorm. In the summer of 1931, a young botanist Nikolai Alexandrovich Avrorin arrived to take his place. On August 26, 1931, at a meeting of research teams, his proposal to create the world's first botanical garden beyond the Arctic Circle was supported. By October 1931, the Polar-Alpine Botanical Garden was officially organized, and Avrorin became its first director. The November session of the USSR Academy of Sciences approved this decision, and the project outlined areas of work that remain relevant even 90 years later.

During the summer season of 1932, the staff of the botanical garden and expeditions conducted the first plantings of specimens obtained from the Botanical Institute of the USSR Academy of Sciences. In 1933, the first greenhouse for plant propagation was built. In 1934, an expedition to Altai was organized, and in 1936, to the Eastern Sayan Mountains. During this period, collection nurseries were established, and an ecological trail was laid on Mount Vudjavrchorr.

Before the war, the garden's staff studied plant biology in the Arctic, identifying decorative and winter-hardy species, and inventorying the flora of the Murmansk region. In 1940, the Polar-Alpine Botanical Garden was recognized as one of the leading botanical gardens in the USSR.

In 1941, Avrorin prepared a guide for landscaping northern settlements, and plants from the garden began to be planted in the Murmansk region. With the onset of the war, work was interrupted, and some staff were evacuated to Syktyvkar. The remaining staff, under Avrorin's leadership, grew food and medicinal plants for the front, developed methods for processing berries, and created technologies for obtaining glucose from lichens. In 1942, biochemist A. L. Kursanov was assigned to Kirovsk, and together with N. N. Dyachkov, they developed the technology for glucose production. An important achievement of the staff was the preservation of collection plants and the herbarium. For the successful organization of work during the war years, Avrorin was awarded the Order of the Red Star.

In 1946, the botanical garden became an independent scientific institution, and the staff increased to 30 employees. In 1951, a plot was allocated for botanical work to the Kola branch of the USSR Academy of Sciences, where the "Experimental Site of the PABSI" is now located. This allowed research to be conducted in different conditions.

In 1960, Avrorin moved to Leningrad, and the garden was directed by Roman Nikolaevich Shlyakov, followed by T. A. Kozupeeva, who led until 1986. In 1967, the garden was granted the status of a research institute, and its structure included four laboratories. In 1981, for its contributions to the development of botanical science, the garden was awarded the Order of the Badge of Honor.

From 1986 to 1998, the garden was headed by G. N. Andreev, and in 1989, a new greenhouse complex was built. In 1998, V. K. Zhirov became the director. In 2002, the garden was named after N. A. Avrorin, and in 2010, the main greenhouse was reconstructed.

Today, the Polar-Alpine Botanical Garden Institute named after N. A. Avrorin is a research institution under the Ministry of Science and Higher Education of the Russian Federation. Its main areas of activity include the introduction and acclimatization of plants, studying the flora and vegetation of Arctic and mountain territories, developing scientific foundations for nature conservation, floriculture and landscaping, as well as popularizing scientific knowledge.