The launch proceeded without any difficulties, although the Blok E stage slightly underperformed and put the spacecraft into a lower-than-intended orbit at 175×222 kilometers versus the normal 181×235 kilometers.

Cosmonaut Valery Bykovsky was originally intended to stay in orbit for 8 days, but the mission details changed many times due to elevated levels of solar flare activity at the time and he was eventually ordered back after five days. This remains the record for solo crewed flight in Earth orbit. In addition, the low orbit of the spacecraft made it uncertain as to whether decay would not occur in under eight days. This combined with solar flare activity affecting the diameter of the Earth's atmosphere might potentially introduce drag that could not only cause premature reentry, but result in Vostok 5 landing almost anywhere on Earth.

Bykovsky performed a couple of simple scientific experiments in orbit and also practiced exercise and testing his body's reactions to weightlessness. In the postflight debriefing, he would say that the overall design of the spacecraft was good, but the clock was in a location that made it hard to see and the instrument panel was placed too far away. The first aid kit could not be reached at all without unstrapping from the seat. Like Valentina Tereshkova, he noted that the helmet headset produced sharp, unpleasant noise. He described the food as generally of good quality, although it probably should not be eaten before launch.