This paper presents a three-dimensional transitional model to describe an innovative design for an air-breathing proton exchange membrane fuel cell (AB-PEMFC) with a microdiaphragm actuated by a piezoelectric device. This newly designed gas pump with a piezoelectric actuation structure is utilized as an air-flow channel in a proton exchange membrane fuel cell (PEMFC) system called PZT-PEMFC. When the actuator moves in the outward direction to increase the cathode channel volume, the air is sucked into the chamber: inward movement decreases channel volume and thereby compresses air into the catalyst layer and enhances the chemical reaction. The air-standard PZT-PEMFC cycle coupling with fuel∕air ratio is proposed to describe an air-breathing PZT-PEMFC. The model is able to simulate its major phenomena and performance in different fuel∕air ratio and PZT frequency. The results show that the PZT actuation leads to a more stable current output, more drained water, stronger suction, and overcome concentration losses at a proper PZT frequency.