In this study, we developed a heterojunction photocatalyst, namely nitrogen-doped carbon quantum dots/titanium dioxide (CQDs/TiO), for the effective and sustainable treatment of ciprofloxacin (CIP) antibiotic in aqueous solution. First, CQDs were prepared from a chitosan biopolymer with a green, facile, and effective hydrothermal carbonization technique and then anchored on the TiO surface via a hydrothermal process. The morphological, structural, and optical properties of the as-prepared materials were characterized by using advanced analytical techniques. The impacts of the mass percentage of -CQDs, catalyst and CIP concentration, and pH on photocatalytic CIP degradation were investigated in depth. Comparative analyses were performed to evaluate different processes including adsorption, photolysis, and photocatalysis for the removal of CIP with TiO and CQDs/TiO. The results revealed that -CQDs/TiO exhibited the highest CIP removal efficiency of up to 83.91% within 120 min using UVA irradiation under optimized conditions (10 mg/L CIP, 0.4 g/L catalyst, and pH 5). Moreover, the carbon source used in the fabrication of -CQDs was also considered, and lower removal efficiency was obtained when glucose was used as a carbon source instead of chitosan. This excellent improvement in CIP degradation was attributed to the ideal separation and migration of photogenerated carriers, strong redox capability, and high generation of reactive oxygen species provided by the successful construction of the CQDs/TiO S-scheme heterojunction. Scavenger experiments indicated that h and •OH reactive oxygen species were the predominant factors for CIP elimination in water. Overall, this study presents a green synthesis approach for -CQDs/TiO heterojunction photocatalysts using natural materials, demonstrating potential as a cost-effective and efficient method for pharmaceutical degradation in water treatment applications.