Amorphous iron oxide/hydroxides with structural disorder can be a potential alternative to typical crystalline structures when applied in environmental nanotechnology. In this work, novel amorphous FeOOH quantum dots (QDs) anchored on boron and nitrogen codoped graphene nanotubes (FeOOH@BNG) with different Fe loadings were synthesized and applied in the degradation of common antibiotic pollutant sulfamethoxazole (SMX). The as-fabricated catalysts were characterized by a series of physicochemical and thermal techniques, revealing the highly dispersive FeOOH QDs on the BNG surface. The as-prepared catalyst shows excellent catalytic ability toward SMX degradation via a Fenton-like approach. The excellent activity of the as-prepared FeOOH@BNG catalysts was ascribed to the enhanced textural properties and better exposure of active sites, thanks to the highly dispersive Fe sites on the BNG supports. The optimal catalyst, FeOOH-5@BNG, was further employed for the optimization of key reaction parameters such as catalyst loading, H2O2 dosage, pH, and reaction temperature. Moreover, electron paramagnetic resonance (EPR) and reactive species quenching tests were employed to reveal the responsive reactive oxygen species and the mechanism in the FeOOH@BNG/H2O2 system for SMX degradation. The current study not only opens new insights into the fabrication of amorphous but metallic nanomaterials but also leads to their potential application in environmental remediation.