An apparatus and method for testing a computer system by utilizing a Field Programmable Gate Array (FPGA) and programmable memory modules is provided. The apparatus includes a controller, a plurality of programmable memory modules, and an FPGA. Each programmable memory module stores configuration data of peripheral devices of the computer system in corresponding versions, respectively, which are differentiated according to functions of the computer system. Each memory module stores configuration data about a PCI host controller, a memory controller, a PLL, an interrupt controller, an arbiter, a UART, or a timer. The FPGA is programmed according to data stored in one memory module selected from among the programmable memory modules. Therefore, in the apparatus, the FPGA does not contain a bus bridge circuit, so that the FPGA has an increased programmable area and can be easily connected even with peripheral devices requiring many input and output ports.