Improvements in the responses of semiconductor gas sensors and reductions in their detection limits toward volatile organic compounds (VOCs) are required in order to facilitate the simple detection of diseases, such as cancer, through human-breath analysis. In this study, we introduce a heater-switching, pulse-driven, micro gas sensor composed of a microheater and a sensor electrode fabricated with Pd-SnO2-clustered nanoparticles as the sensing material. The sensor was repeatedly heated and allowed to cool by the application of voltage to the microheater; the VOC gases penetrate into the interior of the sensing layer during its unheated state. Consequently, the utility factor of the pulse-driven sensor was greater than that of a conventional, continuously heated sensor. As a result, the response of the sensor to toluene was enhanced; indeed, the sensor responded to toluene at levels of 1 ppb. In addition, according to the relationship between its response and concentration of toluene, the pulse-driven sensor in this report can detect toluene at concentrations of 200 ppt and even lower. Therefore, the combination of a pulse-driven microheater and a suitable material designed to detect toluene resulted in improved sensor response, and facilitated ppt-level toluene detection. This sensor may play a key role in the development of medical diagnoses based on human breath.