Heteropolyanions (HPAs) are known as the candidate for an anode redox mediator for redox flow polymer electrolyte fuel cells (PEFCs). The electrochemical properties of HPAs differ depending on the transition elements and heteroatoms in HPAs. For example, heteropolytungstate anions (W–HPAs), in which the transition element is tungsten, have a lower one–electron reduction potential than other HPAs. Therefore, it has been reported that redox flow PEFCs adapted with W–HPAs exhibit high power generation performance. On the other hand, studies on the heteroatoms of HPAs are limited only to electrochemical properties, and statistical and comprehensive studies on the power generation performance of redox flow PEFCs are lacking. Thus, it is beneficial to clarify the optimal heteroatom in order to design anolytes suitable for redox flow PEFCs. In this study, heteropolytungstate anions with different heteroatoms were adapted as anodic redox mediators in a redox flow PEFC. In power generation tests, the redox flow PEFC with an anolyte of zinctungstate anion showed the highest performance. Zinctungstate anion exhibited the fastest reduction and oxidation rates among the W–HPAs investigated in this study.