Naproxen is one of the mostly used drugs worldwide and is most abundant in wastewater. This study aims to adsorb naproxen from wastewater using magnetically modified carbon-based adsorbents. These adsorbents have very large specific area for naproxen adsorption, and magnetite modification provides easy separation and regeneration. The co-precipitation method was used for magnetic modification. Adsorption process was carried out in batches. The effect of adsorption variables was investigated. Langmuir, Freundlich, and Dubinin–Radushkevich isotherms were applied to the equilibrium data. The maximum adsorption capacities of adsorbents from Langmuir isotherm were found as 20.75 mg/g for magnetic multi-wall carbon nanotubes and 87.79 mg/g for magnetic activated carbon. Pseudo-first-order kinetic model, pseudo-second-order kinetic model, intra-particle diffusion model, and Bangham model were used for determination of adsorption mechanisms. The rate-limiting step is electron exchange between the adsorbent and adsorbate. Both film diffusion and intra-particle diffusion occur while the adsorption process. ΔG°, ΔS°, and ΔH° were calculated for the process.