A system and method for filling hydrodynamic bearings with fluid are disclosed. The fluid filling system of the present invention includes a fluid storage tank to store fluid therein, a vacuum vessel to receive a hydrodynamic bearing therein, a fluid dispenser for connecting the fluid storage tank to the vacuum vessel and dripping the fluid into a micro-gap of the hydrodynamic bearing, a pump connected both to the fluid storage tank and to the vacuum vessel and separately exhausting air from both the fluid storage tank and the vacuum vessel to the outside, and a nitrogen storage tank for separately controlling pressure in both the fluid storage tank and the vacuum vessel, wherein the fluid storage tank is pressurized using nitrogen such that the pressure in the fluid storage tank becomes higher than the pressure in the vacuum vessel, thus causing the fluid to move to the vacuum vessel and to be dripped into the hydrodynamic bearing received in the vacuum vessel. The fluid filling system further includes an ultrasonic generator for applying ultrasonic waves to the fluid storage tank, thus removing air bubbles from the fluid.