Launch from the Baikonur Cosmodrome; landing 40 km northwest of Karaganda.

The planned launch on January 13, 1969 was scrubbed due of bad weather. This was the first time in Soviet space history.

The spacecraft docked with Soyuz 5 (Soyuz 4 had the active part). The two spacecrafts were electrical and mechanically connected, but there was no direct way from one spacecraft to the other. It was the first docking of manned spacecrafts. The Soyuz 5 cosmonauts Yevgeni Khrunov and Aleksei Yeliseyev entered the Soyuz 4, in a spacewalk on January 16, 1969 (37m). Yevgeni Khrunov and Aleksei Yeliseyev put on their Yastreb ("hawk") suits in the Soyuz 5 orbital module with aid from Commander Boris Volynov. Yastreb suit design commenced in 1965, shortly after Aleksei Leonov’s difficult EVA. Aleksei Leonov served as consultant for the design process, which was completed during 1966. Suit fabrication and testing occurred in 1967, but the fatal Soyuz 1 accident in April of that year and docking difficulties on the joint Soyuz 2-Soyuz 3 mission delayed its use in space until Soyuz 4-Soyuz 5. To prevent the suit ballooning, Yastreb featured a pulley-and-cable articulation system. Wide metal rings around the gray nylon canvas undersuit's upper arms served as anchors for the upper body articulation system. Yastreb had a regenerative life support system in a rectangular white metal box placed on the chest and abdomen to facilitate movement through Soyuz hatchways. Boris Volynov checked out Yevgeni Khrunov and Aleksei Yeliseyev’s life support and communications systems before returning to the descent module, sealing the hatch, and depressurizing the orbital module. Yevgeni Khrunov went out first, transferring to the Soyuz 4 orbital module while the docked spacecraft were out of radio contact with the Soviet Union over South America. Aleksei Yeliseyev transferred while the spacecraft were over the Soviet Union.

After pressurisation of the Soyuz 4 capsule they were greeted by Vladimir Shatalov. The spacewalkers delivered newspapers, letters, and telegrams printed after Shatalov lifted off to help prove that the transfer took place.

All three cosmonauts landed with the Soyuz 4 spacecraft. Scientific (medical and biological) and technical experiments were also performed, but all in all it were tests of lunar landing techniques. The mission proved it was possible to perform the activities that would be needed on a Soviet lunar landing. The Russian plan called for a lone cosmonaut to land on the moon, return to lunar orbit, then make a spacewalk back from the landing craft to orbiting spacecraft after docking. This was because there was no internal tunnel between the two craft as found on the American Apollo CSM and LM.

The landing was 40 km far from the planned point.

The crew were to meet Leonid Brezhnev during a lavish ceremony at the Kremlin, but this was ruined by an attempted assassination of the Soviet leader. A man shot eight times at the motorcade but aimed at the car containing Georgi Beregovoy, Aleksei Leonov, Andriyan Nikolayev, and Valentina Tereshkova. They were unharmed but Brezhnev's car was forced to speed away past the waiting Soyuz 4 and Soyuz 5 crews on the podium.