Disclosed is a pinhole inspection apparatus, system and method for a membrane electrode assembly of a fuel cell, which can easily detect the position of a pinhole using water and a pH test paper from discoloration caused when the water is in contact with the pH test paper through the pinhole, thus solving the existing problems and allowing the membrane electrode assembly to be reused after the inspection. In particular, a lower fixture is configured to support the membrane electrode assembly and water is uniformly distributed on an upper surface of the membrane electrode assembly. A pH test paper is inserted between the membrane electrode assembly and the lower fixture and discolored upon coming in contact with water that passes through a pinhole in the membrane electrode assembly, thus detecting the presence and position of the pinhole.