A balancing method for balancing at high speed a flexible rotor of a rotary machine, the rotary machine having a stator, and the rotor being supported in the stator by at least two radial magnetic bearings. The balancing method including a step of placing the rotor inside the stator, a step of performing at least one first run in order to identify amplitude and angular location of the unbalance in a first speed range below critical speed, a step of placing first balancing masses inside the rotor on predefined first balancing planes, a step of performing at least one second run in order to identify amplitude and angular location of the unbalance in a second speed range above critical speed, and a step of placing second balancing masses inside the rotor on predefined second balancing planes.