The emerging contaminants such as perfluorinated chemicals (PFCs) have been observed of increasing concerns throughout the world due to their detrimental effects for human health and other creatures in nature. Herein, zirconium imprinted magnetic manganese ferrite assembled reduced graphene oxide (rGO) nanohybrids were used to remove perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS). The effective intercalation of magnetic Zr-MnFe2O4 into rGO was confirmed from FTIR, PXRD, VSM, and Raman spectra. Surface morphologies and particle sizes of as-synthesized adsorbents were determined using FE-SEM, HR-TEM, EDX, and BET analysis. Several factors including contact time, pH, initial concentrations of PFOA and PFOS, type of coexisting anions, and presence of other organic compounds were optimized to determine the maximum density of the prepared Zr-MnFe2O4@rGO nanohybrids. The adsorption of PFOA and PFOS on the Zr-MnFe2O4@rGO nanohybrids was governed mainly by electrostatic attraction followed by hydrophobic interaction. In particular, the treated adsorbents could be easily separated by employing external magnetic force, and it could be regenerated and reused up to four cycles without any significant loss. The Zr-MnFe2O4@rGO nanohybrids are potential candidates for the removal of PFOA and PFOS from aqueous environment.