A system for automatically comparing test points of a PCB includes an application server (1) and a database (6). The application server includes: a PCB file selecting module (10) for selecting a target file and a source file from the database; a test point data extracting module (12) for extracting test point data from the target file and the source file; a table generating module (14) for generating a target table according to the extracted test point data from the target file and generating a source table according to the extracted test point data from the source file; a comparing module (16) for comparing the test point data of the target table and the source table one by one and storing comparison results on those test points which have been modified; and a report generating module (18) for generating a comparison report. A related method is also disclosed.