Catalytic supercritical water oxidation (SCWO) of an organophosphate flame retardant, namely tri-n-butyl phosphate (TNBP) was studied. Firstly, copper oxide nanoparticles (NPs) were synthesized in SCW and their properties were characterized by various analyses. Afterwards, their catalytic performance was investigated under different conditions including reaction temperature (400–500 ◦C), TNBP volume percentage in the feed (1–4%), oxidant ratio (0–2) and reaction time (50–150 min) based on response surface methodology (RSM). The synthesized CuO NPs had an average particle size of 30 nm with a narrow distribution. According to RSM analysis, the reaction temperature and time are the most significant factors; whereas, the impact of the other factors, especially TNBP volume percentage in the feed, was found to be negligible. Overall, excellent performance was achieved under optimal conditions found by the RSM, which was reaction temperature of 500 ◦C, TNBP volume percentage of 4%, oxidant ratio of 1.5, and reaction time of 90 min. The TOC removal efficiency as an indicator of TNBP degradation was about 99%. Finally, in vitro cell viability assays for the cytotoxicity evaluation of fresh and SCW-treated solution were applied. The results of MTT showed that SCWO converts TNBP into by-product that did not induce any cytotoxicity.