Despite substantial efforts to understand the structure of the active site in Fe-based non-precious metal (NPM) catalysts for the oxygen reduction reaction (ORR) in fuel cells, the identification of the active species remains elusive, impeding progress towards the development of highly active and cost efficient catalysts.  We report the isolation and identification of the active Fe species in an NPM catalyst using Cl₂ and H₂ treatments which decrease the heterogeneity of the catalyst. The Cl₂ treatment decreases catalyst activity as shown by a negative shift in the ORR onset of ca. 170 mV.  Subsequent treatment with H₂ restores the initial activity of the catalyst.  Mössbauer spectroscopy and X-ray absorption spectroscopy show many Fe species in the as-prepared catalyst while the catalyst after the Cl₂ and H₂ treatments contains only reduced Fe species encapsulated by C which are highly active for the ORR.