In contrast to the recent immense attention in carbon nitride quantum dots (CNQDs) as a heteroatom-doped carbon quantum dot (CQD), their biomedical applications have not been thoroughly investigated. Targeted cancer therapy is a prominently researched area in the biomedical field. Here, the ability of CNQDs as a selective bioimaging nanomaterial was investigated to assist targeted cancer therapy. CNQDs were first synthesized using four different precursor sets involving urea derivatives, and the characteristics were compared to select the best candidate material for bioapplications. Characterization techniques such as UV-vis, luminescence, X-ray photoelectron spectroscopy, nuclear magnetic resonance spectroscopy, and transmission electron microscopy were used. These CNQDs were analyzed in in vitro studies of bioimaging and labeling using pediatric glioma cells (SJGBM2) for possible selective biolabeling and nanodistribution inside the cell membrane. The in vitro cellular studies were conducted under long-wavelength emission without the interference of blue autofluorescence. Thus, excitation-dependent emission of CNQDs was proved to be advantageous. Importantly, CNQDs selectively entered SJGBM2 tumor cells, while it did not disperse into normal human embryonic kidney cells (HEK293). The distribution studies in the cell cytoplasm indicated that CNQDs dispersed into lysosomes within approximately 6 h after the incubation. The CNQDs exhibited great potential as a possible nanomaterial in selective bioimaging and drug delivery for targeted cancer therapy.