The museum originated from the Cabinet of Natural History, known as the Natural Cabinet, which existed at Kazan University since its founding. The basis of the cabinet consisted of zoological and mineralogical collections gathered in the late 18th century for the Yekaterinoslav University, which was never opened. Initially, the cabinet was headed by Professor K. F. Fuchs, and in 1825 and 1828, by E. I. Eichwald. During this period, the collections were actively replenished: astronomer I. M. Simonov donated samples of flora and fauna from the Southern Hemisphere, collected during the Bellingshausen and Lazarev Expedition, and Eichwald brought zoological specimens from his trip to the Caspian Sea in 1825 and 1826.

From 1828, the cabinet was headed by Professor E. A. Eversman, who managed it until 1860. Under his leadership, the zoological part of the cabinet became an independent institution with a systematic approach, and the collections were significantly enriched with both exotic species from Germany and Russian fauna collected by Eversman in the Aral-Caspian region. In 1837, the personal collection of mammals and birds of K. F. Fuchs from the Kazan province was acquired. According to A. A. Ostrooumov, by 1844, the museum had 5735 exhibits, including 1900 insects, 1445 shells, 1402 stuffed birds, and 227 stuffed mammals. Over the next ten years, the collection increased by another 400 exhibits. The museum was popular among the townspeople, who often visited it on holidays.

In 1871 and 1897, the cabinet was headed by Professor N. M. Melnikov. In 1881, A. M. Butlerov donated his collection of butterflies, which included over a thousand species, to the university. In 1897 and 1925, the cabinet was managed by Professor A. A. Ostrooumov, under whom the collections continued to grow, catalogs of birds and fish were created, and research was conducted on the sturgeon, which disappeared in the early 1920s.

In the 1840s, a zootechnical cabinet was established at the university, and in 1945, the zoological and zootechnical cabinets were merged into the Zoological Museum. In 1991, a botanical department was added to the museum, which for a long time was accessible only to specialists and students. In 2002, the museum was named after E. A. Eversman.