This study describes the preparation, characterization and application of Fe3O4/graphene quantum dots (Fe3O4/GQDs) magnetic nanocomposite as a novel adsorbent for magnetic solid phase extraction (MSPE). The Fe3O4/GQDs was synthesized by a simple hydrothermal method and the resultant nanocomposite was characterized by X-ray powder diffraction, field emission scanning electron microscopy and Fourier transform infrared spectroscopy. The prepared nanocomposite was used for the preconcentration and determination of bisphenol A (BPA) in drinking water samples using high performance liquid chromatography with ultraviolet detection (HPLC-UV). Under optimal extraction and analytical conditions, the developed method demonstrated a wide dynamic linear range (0.1–300 ng mL−1), good linearity (R2 = 0.9958), low detection limit (12.3 pg mL−1) and a high enrichment factor (360). The developed MSPE-HPLC-UV method was successfully applied for the determination of leaked BPA from plastic bottles into drinking water samples after exposing it to sunlight. Satisfactory recoveries showed that the matrices under consideration do not significantly affect the extraction process. The adsorption efficiencies of Fe3O4/GQDs, Fe3O4/graphene and unmodified magnetic Fe3O4 nanoparticles were comparatively studied for the preconcentration and determination of BPA by HPLC-UV. Based on experimental results, Fe3O4/GQDs exhibit improved adsorption behaviour because of the unique surface properties of GQDs.