The design was conceived in 1978 when Myasishchev was asked to solve the problem of transporting rockets and other large space vehicles to the Baikonur Cosmodrome. Engineers used an old 3M (a modified M-4 bomber) and replaced the empennage with dihedralled horizontal stabilizers with large, rectangular end-plate tailfins to accommodate payloads measuring as large as twice the diameter of the aircraft's fuselage. A large, aerodynamically optimized cargo container, placed on top of the aircraft, would contain the freight. In addition, a new control system was added to the plane to compensate for the added weight.
The Atlant first flew in 1981 and made its first flight with cargo in January 1982. Its main task was to ferry Energia rocket boosters from their development plant to the Baikonur Cosmodrome. On several occasions, the then-incomplete Soviet space shuttle Buran was piggybacked to the Cosmodrome as well.