The present invention features a pinhole detection system of a fuel cell that preferably includes a stage on which a fuel cell element unit is disposed to be detected, a drive portion that is configured to move the stage so as to rotate the fuel cell element unit, a X-ray source that is disposed at one side of the stage to apply X-ray to the fuel cell element unit that rotates, an image detector that detects X-ray penetrating the fuel cell element unit, and a computer tomography that reconstructs tormogram that is detected by the image detector to a three dimension. Preferably, the fuel cell element unit is rotated on the stage, X-ray is applied to the rotating unit to gain the tomogram thereof, and the tomogram is reconstructed to be a three-dimensional image through a computerized tomography (CT scanning) such that the pinhole formed within the unit can be effectively detected.