The degradation of lignin in oil palm empty fruit bunch (EFB) fibers by a low concentration of H2O2 was observed with the assistance of Fenton oxidation with Fe(III), Fe(0), and Fe3O4 as a catalyst. To escalate the oxidation activity toward lignin in the EFB fibers, the uptake of the Fenton reagent on the EFB fibers for in situ Fenton oxidation was optimized with fitted Langmuir and Freundlich adsorption models. The efficiency of assisted Fenton reagents was monitored through controlled parameters of H2O2 concentration, retention time, and increment of Fenton reagents. The delignification was observed with up to 71.2% of lignin degradation compared to 47.2% without the use of the Fenton reagents. The characteristics of EFB fibers after the oxidation process were changed based on the observation of morphological and chemical properties. The oxidation concurrently dislodged part of the silica bodies and disrupted specific functional groups and the crystallinity of the EFB fibers.