Nowadays, food waste valorization is under intense worldwide investigation. In this framework, bioactive compounds from papaya seeds were recovered by supercritical extraction to evaluate the process variables effect in extraction kinetics. A computational code MSEM (MatLab Simulation Extraction Models) was developed to represent different mass transfer models used to describe extraction curves, with best performance by Sovova's model. The constant extraction rate period provided the highest phenolic content, confirming the high value of papaya seed as source of bioactive compounds such as benzyl isothiocyanate. Moreover, the scale-up criterion with constant ratios of m(solv)/M and Q(CO2)/MA between small and large scales was suitable. The MSEM code, validate by the small scale data, was efficiently applied to represent the large scale kinetic curves, and also to predict the kinetics behavior at different conditions, based on small scale parameters, enabling the description of the extraction curves without experimental data.