A 3-D FEM (Finite Element Method) analysis of the turbo-blower shaft attached to a fuel cell was performed using Lanczos algorithm. The modal analysis was analyzed in order to investigate natural frequency and maximum displacement for 10 times. It was found that the first mode of natural frequency is 109.1Hz with the maximum displacement of 0.16mm while the tenth mode of natural frequency is 2464Hz with the maximum displacement of 0.25mm. Consequently, the results of modal analysis of the turbo-blower for a fuel cell system show good dynamic responses.