The Museum of History of the Krasnoyarsk District was established by the decree of the head of the district administration No. 1093 on August 9, 1999. In 2001, according to the administration's decision No. 953 from August 1, it received the status of a municipal museum.

In the same year, a department of nature and archaeology was opened, the concept of which was developed in collaboration with the Samara Regional Museum of Local History named after P. V. Alabin. In 2002, after studying archival documents, an expedition was conducted to the village of Stara Binaradka, where a camp and cemetery of German prisoners of war were discovered.

The museum covers the entire history that is of interest to the residents of the Krasnoyarsk District. In the late 1990s, an organizing committee was created to oversee the establishment of the museum, led by Yuri Vasilyevich Brykov, a methodologist at the district center for children's and youth creativity. The committee included Valentina Alexeyevna Kuzurina, Ivan Kirillovich Sidorov, Natalia Ivanovna Kosyreeva, Yuri Andreevich Penner, Alexey Gennadyevich Bushov, and Svetlana Nikolaevna Zhadnova. The work began with inquiries to museums in the European part of Russia, where combat operations took place during the Great Patriotic War, to establish the burial sites of Krasnoyarsk residents. Many museums responded, providing documents that helped create collections primarily dedicated to the Great Patriotic War. A space of over one hundred square meters was allocated for the museum in a district school.

At the same time, a scientific research expedition was conducted in the district, involving museum staff and leaders of school local history clubs. The museum director, Yuri Brykov, traveled to Volgograd to coordinate the participation of Krasnoyarsk residents in a military field expedition to search for the fallen at Stalingrad. From 2002 to 2004, four expeditions were conducted, during which the remains of 200 soldiers were exhumed and reburied.

The first exhibits of the museum included clothing, memories, documents, and photographs. The main task was to preserve memory, which became the impetus for creating the museum. To replenish the collections and promote patriotic education among the population, four expeditions to the Volgograd region and one to Smolensk were organized as part of the "Memory" campaign, involving 50 participants.

In 2003, in collaboration with the Samara Regional Museum, the historical battle on the River Kondurcha between Timur Tamerlane and the Khan of the Golden Horde Tokhtamysh was reconstructed, marking the beginning of the decline of the Golden Horde.

As a result of ethnographic expeditions, a cadastral survey of monuments was compiled for the Department of Culture of the Samara Region. Scientific research led to the discovery of unique monuments important for the development of the district, such as the monument to teacher Serafimov, a burial site in the village of Hilkovo, and the remains of a redoubt in the village of Gundorovka.

To study natural and architectural monuments on the River Sok, a water expedition was organized with the participation of 18 members of the children's youth association "Krasnoyarsk Local Historian." The collected materials formed the basis for the book "Journey along the River Sok" and the development of tourist routes.

In 2004, an expedition was organized to the village of Krasny Gorodok, where there was a boarding school for disabled veterans of the Great Patriotic War. Despite difficulties in finding participants from those years, the memories of the boarding school staff were recorded. A video segment about the Rakov Women's Monastery was also filmed. The expedition involved 26 people from various villages.

In the winter of 2004 and 2005, a film was made about the Popov Radio Station, built during the war years. Former positions of anti-aircraft batteries around the village of Novosemeikino were found. An exhibition about the radio station was created in the museum.

In the same year, an exhibition titled "Models of Military Equipment" was opened, dedicated to the 60th anniversary of Victory. Residents of the village of Krasny Yar actively participated in assembling models. Museum staff filmed video material about veterans and workers on the home front, as well as military facilities in the district. During the work, they met pilot Pyotr Amosov, awarded the medal "For the Liberation of Belgrade."

On May 9, a presentation of the film "Oh, Frontline Paths" took place in the villages of Krasny Yar and Belozerki, dedicated to Victory Day. The full version of the film was shown for the 61st anniversary of Victory.

At the "Museum Picnic" festival in Tolyatti, an exhibition titled "The Hardware Store of Stekolsikov" was held, and at the "Battle on the River Kondurcha" festival, a model of the Krasnoyarsk Fortress was presented.

The museum acquired a collection of watercolor paintings by artist Gainullin, dedicated to the natural and memorable places of the district.