Water management inside a proton exchange membrane fuel cell (PEMFC) is an important issue for improving the performance of a PEMFC. It is necessary to understand water transport phenomena inside a PEMFC for water management. Especially humidity measurement near the membrane electrode assembly is indispensable. In order to measure the humidity, we fabricated the capacity type humidity sensor with thickness of 7 μm using micro-electro-mechanical system techniques. In addition, in order to measure the humidity locally, we reduced the parasitic capacitance by changing the shape of the sensor, and improved the sensitivity of the sensor by carrying out O2 plasma etching on the humidity sensitive layer. Finally, the improved sensor was inserted between the catalyst layer and micro porous layer inside a PEMFC, and the humidity inside it during power generation was measured to confirm that the sensor was functioning.