Balancing method for balancing at high speed a rotor of a rotary machine comprising a stator and a rotor having a rotational axis (X-X) and supported in said stator by two radial magnetic bearings (22, 24), the stator comprising a casing having an opened end and a top cover adapted to close the opened end of the casing and the rotor comprising an upper and a lower shaft (16, 18), characterized in that the balancing method comprises: - a step of placing the rotor in the casing of the stator, - a step of performing one first run, in which the rotor is rotated on until a first threshold, the radial magnetic bearings are operated in a synchronous force rejection mode, the rotor is rotated until a second threshold, and amplitude and the angular location of the unbalance in a speed range comprised between the first and second threshold is identified, according to information received from an electronic control device controlling the radial magnetic bearings, - a step of removing the top cover and of placing first balancing masses (72, 78) inside the rotor against the inner cylindrical surface (16c, 18c) of the rotor, the first balancing masses (72, 78) being disposed on predefined first balancing planes (82, 88) defined in a cartography associated to the rotor, said first balancing planes (82, 88) being associated to each of the rotor shafts (16, 18), - a step of closing the upper part of the stator casing by the top cover, - a step of performing one second run, in which the rotor is rotated until the first threshold, the radial magnetic bearings (22, 24) are switched to the synchronous force rejection mode, the rotor is rotated in the synchronous force rejection mode until a second threshold, the radial magnetic bearings (22, 24) are switched to an active resonance damping mode, the rotor is rotated until a third threshold in resonance damping mode, the radial magnetic bearings (22, 24) are switched to a synchronous force rejection mode, the rotor is rotated until a fourth threshold in synchronous force rejection mode, and amplitude and the angular location of the unbalance in a fourth speed range R4 comprised between the third and fourth thresholds is identified, according to information received from an electronic control device controlling the radial magnetic bearings, - a step of removing the top cover and of placing second balancing masses (74, 76) inside the rotor against the inner cylindrical surface (16c, 18c) of the rotor, the second balancing masses (74, 76) being disposed on predefined second balancing planes (84, 86) defined in a cartography associated to the rotor, said second balancing planes (84, 86) being associated to each of the rotor shafts (16, 18). - a step of placing the rotor in the casing of the stator, - a step of performing one first run, in which the rotor is rotated on until a first threshold, the radial magnetic bearings are operated in a synchronous force rejection mode, the rotor is rotated until a second threshold, and amplitude and the angular location of the unbalance in a speed range comprised between the first and second threshold is identified, according to information received from an electronic control device controlling the radial magnetic bearings, - a step of removing the top cover and of placing first balancing masses (72, 78) inside the rotor against the inner cylindrical surface (16c, 18c) of the rotor, the first balancing masses (72, 78) being disposed on predefined first balancing planes (82, 88) defined in a cartography associated to the rotor, said first balancing planes (82, 88) being associated to each of the rotor shafts (16, 18), - a step of closing the upper part of the stator casing by the top cover, - a step of performing one second run, in which the rotor is rotated until the first threshold, the radial magnetic bearings (22, 24) are switched to the synchronous force rejection mode, the rotor is rotated in the synchronous force rejection mode until a second threshold, the radial magnetic bearings (22, 24) are switched to an active resonance damping mode, the rotor is rotated until a third threshold in resonance damping mode, the radial magnetic bearings (22, 24) are switched to a synchronous force rejection mode, the rotor is rotated until a fourth threshold in synchronous force rejection mode, and amplitude and the angular location of the unbalance in a fourth speed range R4 comprised between the third and fourth thresholds is identified, according to information received from an electronic control device controlling the radial magnetic bearings, - a step of removing the top cover and of placing second balancing masses (74, 76) inside the rotor against the inner cylindrical surface (16c, 18c) of the rotor, the second balancing masses (74, 76) being disposed on predefined second balancing planes (84, 86) defined in a cartography associated to the rotor, said second balancing planes (84, 86) being associated to each of the rotor shafts (16, 18).