This paper reports a new micromachined flow-through polymerase chain reaction (PCR) chip for applications of rapid pathogen diagnosis. The PCR chip comprised a micro thermal control module and a microfluidic control module fabricated using MEMS (micro-electro-mechanical-systems) technology. The micro thermal control module was formed with three individual heating and temperature-sensing sections, each modulating a specific temperature for denaturation, annealing and extension process, respectively. The membrane-activated micropumps were used to transport sample fluids through three reaction regions to adjust the time ratio and cycle numbers for PCR. The experimental results showed that S. pneumoniae detection gene (273 bps) could be amplified successfully using the new flow-through PCR chip. The new PCR chip could be promising for rapid clinical diagnosis of DNA-based infectious disease.