We developed a new type hydrogen sensor for a proton pumping gate FET with a triple layer of Pd / proton conducting polymer / Pt. Compared with conventional type FET with a single catalytic metal gate, the selectivity was improved. Furthermore, two different output signals of DC and AC modulation were obtained. According to increments of the upper gate voltage to a lower gate, the sensitivity was increased. When modulation voltage was added to the upper gate voltage, AC modulation output was obtained. The response mechanism of the new type FET was investigated using several hydrogen gases and with modulation conditions. Consequently, the hydrogen response mechanism can be explained by a hydrogen dissociation reaction occurring at the upper gate, and the hydrogen gas and generated proton can pass through the proton conducting polymer, and finally an equilibrium hydrogen reaction occurs at the lower gate. These complex mechanisms can be controlled by the gate bias and modulation voltage.