To electrochemically control structural and transport properties of oxygen-deficient perovskite SrFeO _y (2.5 ≦  y ≦ 3) (SFO) epitaxial films, we employed electric-field-effect transistor structures in which the proton-conducting solid electrolyte Nafion is used as a gate insulator. When a positive gate voltage ( V_GS) is applied and protons are injected toward the film channel layer, the SFO films are electrochemically reduced, leading to increases in the channel resistance. On the other hand, when a negative V_GS is applied and protons are removed, the SFO films are oxidized, and as a result, the channel resistances decrease. In addition, we found that the electrochemically reduced SFO films accommodate protons, forming the proton-containing oxide H _xSrFeO_2.5 whose proton concentration is determined by elastic recoil detection analysis to be x ∼ 0.11. Our results indicate the usefulness of the proton-conducting solid electrolyte for electrochemically controlling transition metal oxides and for exploring proton-containing oxides.