In 1864, the Yaroslavl Natural History Museum was founded, which included collections on botany, zoology, mineralogy, and geology. In 1881, it became accessible to the general public. In 1895, thanks to the Yaroslavl Provincial Scientific Archive Commission, a museum of cultural and historical profile was established, known as the Ancient Repository. In 1909, the Yaroslavl Art Society was formed, uniting artists, teachers from the Demidov Lyceum, and local historians. It organized exhibitions, published albums on architectural monuments of Yaroslavl, and held lectures on visual arts, striving to create an art museum or gallery. In 1913 and 1914, the St. Petersburg Academy of Arts transferred 14 works by Russian masters to the fund, and by 1918, there were about 30. The collection was supplemented with works from local exhibitions and donations from private individuals, stored in the Ancient Repository of the Yaroslavl Provincial Archive Commission.

With the advent of Soviet power, a new stage in the development of museum affairs in Russia began. In November 1917, the All-Russian Collegium for Museum Affairs and the Protection of Monuments of Art and Antiquity was established under the People's Commissariat for Education. Museums began to perform an ideological function, shaping the worldview of the new Soviet person. In 1919, the building of the former Spiritual Consistory, built in 1815 by architect L. Ruski, was transferred for use as a gallery. In 1919 and 1924, the gallery was under the jurisdiction of the Yaroslavl Provincial Subdepartment for Museum Affairs. Its collection included works formed by Yaroslavl public organizations before the revolution. During the Yaroslavl Uprising, the gallery building was severely damaged and needed repairs. In March 1920, part of the collection was exhibited at the Yaroslavl Great Manufactory. The gallery collected both classical art and works by contemporary artists of the early 20th century. In 1922, the museum was granted the status of a Museum of Ancient Russian Art, and its fund was replenished with items looted from Yaroslavl churches in July 1918 and closing temples. In 1924, the museums of Yaroslavl united into the Yaroslavl State Regional Museum, which included the Natural History Museum, Museum of History and Everyday Life, Museum of Books, scientific library, Art Gallery, and Museum of Ancient Russian Art. This allowed specialists to combine efforts without infringing on the specialization of the museums. The Art Gallery and the Museum of Ancient Russian Art became a single organism, uniting the art fund of Yaroslavl.

Visitor registration for the gallery began in 1922 and by 1928 numbered over 40,000 people. All areas of museum activity developed: scientific research, restoration, exhibition, propaganda and educational work, excursions, lectures, and practical classes with students. Under A. I. Malygin, who led the gallery until 1929, all artistic forces of the city rallied around it. At that time, an exhibition of Russian art of the 18th century and the first decades of the 20th century was formed. In 1927, 56 works were received from the State Museum Fund. By the beginning of 1928, the collection numbered about 1,600 exhibits: 335 paintings, 149 watercolors and drawings, 874 engravings and lithographs, 34 sculptures, and 194 items of applied art.

In the second half of the 1920s, inspections by the Main Political Department began in Yaroslavl, leading to persecution of older specialists. From January 1929 to March 1936, Yaroslavl was part of the Ivanovo Industrial Region. The status of the Yaroslavl Museum changed three times, which negatively affected its development. Valuable employees were dismissed, and the collection was moved to the premises of the historical museum. In 1930 and 1931, the collection was closed to the public. In 1932, the museum became the Yaroslavl Regional Local History Museum, while the gallery existed as its department. It was tasked with forming a collection of socialist realism works. In the new exhibition of the art department, located in the halls of the former Metropolitan Chambers, until 1936, works of various directions were exhibited, but 19th-century art was presented as imperialistic, while works by futurists of the 20th century were deemed alien to socialist ideology.

In March 1936, it was decided to restore the Yaroslavl region. In 1937, the gallery received the status of an independent Yaroslavl Regional Museum of Arts. In 1941 and 1945, the museum practically did not function due to the Great Patriotic War. In 1936, repressions began, and lists of authors whose works were to be confiscated were sent to the museum. Many artists, such as A. M. Kadak, N. P. Evdokimov, and S. V. Shcheglov, fell under repression. Their works nearly disappeared, but some pieces were hidden by museum staff in storage. In the 1980s, works by repressed artists, such as F. I. Veseli, B. A. Petrukhin, and A. A. Derzhavin, were introduced into the collection. During the war, the museum was closed, the building was transferred to the Military Department, and the collection was partially evacuated. After the war, the museum resumed its exhibition activities. In June 1946, a permanent exhibition of Russian art opened, and in November, the halls of Soviet period art. From the late 1940s, the museum began to be called an art museum, and this was officially confirmed in 1950.

In 1953, art museums, including the Yaroslavl one, came under the jurisdiction of the Department of Fine Arts and the Protection of Monuments of the Ministry of Culture of the RSFSR. They were tasked with demonstrating Russian and Soviet realistic art. In the 1950s, a restorer, Elena Pavlovna Yudina, became the first qualified specialist in painting restoration in Yaroslavl. She saved numerous works, trained students, and in 1971 created a scientific restoration department. The exhibition reflected the development of domestic art from the 18th century to the mid-1950s. The collection of the Soviet period was weak, and the removal of works by repressed artists diminished it. In 1956, a guide by V. P. Mitrofanov was published, and in the 1950s and early 1960s, descriptions of about 1,300 museum items were compiled. Based on this, the first illustrated catalog of the museum was released.

In the late 1950s, the collection moved to the premises of the former Spaso-Preobrazhensky Monastery. At that time, the collection included 745 units of painting, 2,768 graphics, and 116 sculptures. In 1959, the State Yaroslavl-Rostov Historical, Architectural, and Art Museum-Reserve was established, uniting the museums of Yaroslavl and Rostov, including the regional art museum. This limited its development and slowed the replenishment of the collection. By the end of the 1960s, the idea of restoring the independence of the art collection emerged, and in 1969, the museum received independent status. In 1970, it was allocated a mansion on the Volga embankment, where the collection is exhibited today. The majority of the collection was preserved, and obtaining independent status opened new prospects for the museum.