Photodynamic therapy (PDT) emerged as a promising cancer therapeutic technique due to the prospect of triggering and controlling the drug action with light, which will reduce the detrimental side effects of traditional chemotherapy. In recent years, in PDT drug design, progressive approaches such as the use of nanocarriers and targeted delivery systems have been achieved to improve the bioavailability and efficacy of the therapy. Herein, we report the synthesis, photophysical, and photobiological properties of a graphene oxide quantum dot (GQD)− BODIPY nanoconjugate (GQD−BDPA), which exhibits excellent water solubility, high triplet and singlet oxygen generation yields, and high PDT efficiency. Green luminescent GQDs were synthesized from graphene oxide via a modified acid treatment method, and the amino BODIPY derivative (BDPA) was covalently attached to the GQDs via 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide−N-hydroxysuccinimide coupling. This nanoconjugate, with average lateral dimensions of ∼50 nm, exhibited characteristic absorption and fluorescence properties of both GQDs and BDPA. The triplet quantum yield of GQD−BDPA was found to be 0.94 ± 0.02 with a remarkable singlet oxygen generation efficiency (90%), demonstrating the potential of this nanoconjugate for PDT applications. In vitro PDT activity of this nanoconjugate was studied using MDA-MB-231 cancer cell lines and GQD−BDPA is found to be an efficient system for PDT treatment with an IC 50 value of 30 nM (sensitizer concentration). The apoptotic cell death was characterized and confirmed using various assays such as the tetramethylrhodamine methyl ester assay, the Annexin V apoptotic assay nuclear condensation, etc., on MDA-MB-231 cell lines. The water-soluble GQDs surpass the solubility and bioavailability issues of traditional sensitizers and this covalent-nanoconjugate approach enhances the local cellular concentration of the BPDA photosensitizer, realizing a useful strategy for efficient PDT applications.