A system and method for measuring a magnetocardiogram (MCG) in order to measure a weak magnetic field generated from the heart of a small animal such as a laboratory rat are provided. The system includes a case, a SQUID sensor located and fixed inside the case to detect magnetism, a platform arranged near the SQUID sensor inside the case, the small animal being placed on the platform, a linear station to which the platform is fixed to move a location of the platform, and a control unit configured to control operations of the SQUID sensor and the linear station and measure the MCG of the small animal using intensities of the magnetism detected by the SQUID sensor.