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This study develops an air breathing pump driven by a piezoelectric actuator for a proton exchange membrane fuel cell (PEMFC) stack. Permanent magnets are combined with a piezoelectric actuator to drive three air breathing pumps using magnetic force. This design enables the pump to provide a sufficient amount of air simultaneously to six cathode flow field plates in a stack of three “bi-cell PZTmag–PEMFCs”. When both the PZTmag and the PDMSmag had a magnet with a 6-mm diameter and 1-mm thickness, a maximum amplitude of 87 μm was generated at 0.03 W of power under operating conditions of 70 Hz and 40 V. In computational fluid dynamics (CFD), when the nozzle and the diffuser of an air breathing pump have an aspect ratio of 13.13, air flow distributes uniformly inside the pump, thus allowing for uniform transmission of oxygen to the membrane electrode assembly. This aspect ratio was applied to the bi-cell PZTmag–PEMFC stack and yielded a maximum net power flux of 0.1925 W·cm−2, 20% higher than that reported in a previous study (Ma, 2013), with 68% and 76% less volume and weight, respectively.