A mixture of ferrous ions and hydrogen peroxide, known as Fenton's reagent, is an effective oxidant and has been widely used in various industrial applications; however, there is still controversy about what the oxidizing agents are and how they are produced. In this study, we have determined minimum free-energy paths (MFEPs) from Fenton's reagent to possible oxidizing agents such as hydroxyl radicals and ferryl-oxo species by combining ab initio molecular dynamics simulations and an MFEP search method. Along the MFEPs, representative free-energy profiles of the Fenton reaction were elucidated. On the basis of the free-energy profiles, we revealed that the reaction producing ferryl-oxo species from Fenton's reagent is more energetically favorable than that yielding a free hydroxyl radical, by 24.4 kcal mol(-1), which indicates that the ferryl-oxo species is the primary oxidizing agent in reactions of Fenton's reagent. Moreover, we clarified that the ferryl-oxo species is favorably formed via a two-step reaction pathway, which reaches the product through a dihydroxyiron(IV) intermediate. The energetics charting the free-energy profiles provided valuable information for a comprehensive understanding of Fenton reactions. We concluded that a ferryl-oxo species produced from Fenton's reagent serves as the primary oxidizing agent in the Fenton reaction.