Graphene quantum dots (GQDs) have gained enormous attention due to their unique optical properties and emerging employment in biology. Herein, we report the synthesis of highly crystalline GQDs having superior physicochemical and near infrared (NIR)-responsive properties using simple waste, withered leaves of Ficus racemosa, an Indian fig tree, as a carbon source. A considerably large production yield was obtained (ca. 18%) with a competitive quantum yield of 14.16%. The GQDs exhibited excellent dispersibility in both organic as well as aqueous solvents and were highly photostable. High-resolution transmission electron microscopy showed the presence of ultra-small honey-combed as well as self-assembled GQDs. Cell cycle analysis using flow cytometry and biocompatibility studies showed that the GQDs were cytocompatible and were used as in situ labeling probes for normal as well as cancer cells. Furthermore, upon irradiation with an 808 nm laser (0.5 W cm⁻²), a concentration-dependent photothermal response and production of reactive oxygen species were observed. Confocal laser scanning microscopy showed that GQDs did not lose their fluorescence despite continuous laser irradiation (30 min) on MDA-MB-231 breast cancer cells. Thus, cell death could be traced using GQD-labeled MDA-MB-231 cells post-therapy using the photostability of GQDs, unlike photo-bleachable organic dyes. Thus, a low-cost, scalable, green-synthesis of GQDs with highly efficient optical properties will pave the way for new therapeutics and imaging in biomedical cancer research.