A system for automatically testing motherboards includes a test server (1), client computers (2), and a network (5) connecting the test server with the client computers. The test server is for storing a plurality of high-level OSs (Operating Systems), test programs and test script files, for setting contents of test configuration files, and for storing test results. Each client computer has a motherboard installed therein, and is operated under a DOS (Disk Operating System). The client computer downloads and installs a high-level OS from the test server, downloads and installs one or more test programs and a test script file according to a test configuration file set by the test server, executes the test script file to auto-run test programs in a sequence specified in the test configuration file, and then transmits test results to the test server.