A system and method for filling hydrodynamic bearings with fluid. The fluid filling system includes a vacuum vessel for receiving the hydrodynamic bearing therein, a pump hermetically connected to the vacuum vessel and exhausting air from the vacuum vessel to the outside, an ultrasonic generator for generating vibrations in the vacuum vessel, and a fluid dispenser for dripping the fluid into the hydrodynamic bearing. When air is exhausted from the vacuum vessel to the atmosphere by the pump, the hydrodynamic bearing is vibrated by the ultrasonic generator and air is exhausted from a micro-gap between the shaft and sleeve of the bearing the atmosphere.