In vertical positioning systems, the friction force and the gravity load cause significant error. In order to minimize the effect of friction and gravity load, this paper presents the noncontact gravity compensator applying magnetic fluid seals. The structure of the magnetic fluid seals was proposed for the linear motion system, and the dimensions of the magnetic fluid seal components were determined based on the result of the magnetic field analysis using FEM. Magnetic field analysis was used in order to investigate the relationship between the seal capacity and varied dimensions. Based on the results of the analysis, several types of magnetic fluid seal units were manufactured, and the analytical results were compared with the results of the seal capacity evaluation experiment in order to confirm the validity of the magnetic field analysis. In addition, the gravity compensating system using the magnetic fluid seals was constructed and applied to a vertical positioning system. Positioning resolution was evaluated with stepwise positioning experiments. Tracking performance and the response of the pressure were evaluated by the continuous path control experiment. According to these experimental results, the effectiveness of the gravity compensator with magnetic fluid seal was confirmed.