In this study, a composite material consisting of three-dimensional graphene aerogel and iron oxide nanoparticles (3DG/Fe3O4) was created and utilized for the purpose of magnetic solid-phase extraction (MSPE) of thirteen polycyclic aromatic hydrocarbon (PAH) compounds via gas chromatography–mass spectrometry/selected ion monitoring (GC-MS/SIM) analysis. The synthesized adsorbent underwent a range of characterization techniques, including scanning electron microscopy, vibrating sample magnetometry, Raman spectroscopy, X-ray diffraction, Brunauer–Emmett–Teller, Fourier transform-infrared spectroscopy, and Barrett–Joyner–Halenda techniques, to examine its properties and morphology. The synthesized adsorbent integrates the benefits of superior adsorption capacity from modified graphene oxide (GO) with the magnetic separability of magnetite microparticles, resulting in a high adsorption capacity with easy separation from sample solutions. The efficiency of the proposed method was optimized and modeled using a central composite design (CCD), which considered the primary factors influencing it. The optimal conditions were obtained as the adsorbent dosage of 10 mg, the extraction time of 4 min, and the salt concentration of 3% w/v. The limit of detection for the target PAHs was established to range from 0.016 to 0.2 ng mL−1 in optimal conditions, exhibiting a signal-to-noise ratio of 3. The linear dynamic range spanned from 5 to 100 ng mL−1, with determination coefficients (R2) ranging from 0.9913 to 0.9997. The intra- and inter-day precisions were calculated as relative standard deviations (RSDs) equal to 3.9% and 4.7%, respectively. The proposed method was successfully applied to the determination of PAHs in water samples (tap, river, and rainwater), and recoveries in the range of 71–110% (RSDs < 5.2%, n = 3) were obtained.