Deoxyhypusine hydroxylase is a critical enzyme for hypusination of eukaryotic translation initiation factor 5A (eIF5A). Human deoxyhypusine hydroxylase (hDOHH) has a nonheme diiron active site that resembles both in structure and function of those found in methane and toluene monooxygenases, bacterial and mammalian ribonucleotide reductases, and stearoyl acyl carrier protein Δ9-desaturase from plants. However, the detailed catalytic mechanism of hDOHH is still unclear. In this work, extensive DFT calculations reveal that the catalytic mechanism of hDOHH consists of four consecutive steps: (1) peroxo isomerization triggered by substrate binding; (2) rate-determining O-O bond cleavage and formation of the [FeIV2(μ-O)2]4+ compound; (3) H atom abstraction from the substrate; and (4) OH rebound to the substrate. This work not only rationalizes the exceptional stability of the diiron(iii)-peroxo complex in hDOHH, but also confirms that hDOHH uses a diamond shape [FeIV2(μ-O)2]4+ core to complete crucial H atom abstraction from the substrate. Our DFT calculations exclude the reaction pathway of hDOHH to use diiron(iii)-peroxo species to directly react with the substrate.