In this study, the combined synergetic influence of H2O2 emulsification with the addition of multi-walled carbon nanotubes (MWCNT) to B20 biodiesel blend is ascertained on the exhaust emissions and performance of a compression ignition engine. Methyl ester obtained from waste cooking oil is used to prepare B20 blend. Variation in the concentrations of H2O2 (0.5%, 1%, 1.5%) and MWCNT (0, 20, 40 ppm) was carried out at 50%–100% of the full load condition. Increasing the concentrations of H2O2 and MWCNT positively affect the emissions of CO, HC, and Smoke, wherein a maximum reduction of 52%, 30.2%, and 16.1%, respectively, was achieved. Similarly, the average increase in brake thermal efficiency and an average reduction in brake specific fuel consumption is seen to be 10.3% and 9.1%, respectively. An increasing trend for NOx was seen with the increase in the MWCNT concentration (average increase by 10.2%). However, H2O2 emulsification resulted in an average decrease of 21.5%, indicating that H2O2 had a more dominating effect due to hydroperoxyl radicals. Fitting models between the controlling factors and the response of emissions and performance parameters were developed using an artificial neural network (ANN) (R2 > 0.99). From studying the interaction of H2O2 and MWCNT using ANN-derived response surface plots, it is seen that H2O2 emulsification dominated the effect of MWCNT nanoparticles for the responses of CO, HC, Smoke, NOx, and BTE.