In the present work an attempt was made to reduce the NOx emission of crude rice bran oil methyl ester (CRBOME) with a marginal increase in smoke density and decrease in brake thermal efficiency in a stationary CI engine. Three factors namely fuel injection timing, quantity of exhaust gases recycled and fuel injection pressure were chosen. Experiments were designed by employing design of experiments method and tests were conducted with combination of factors as per Taguchi’s L9 orthogonal array. Percentage contribution of each factor and the most influencing factor in controlling the response variables (NOx emission, smoke density and brake thermal efficiency) were obtained through ANOVA. Multi-response signal-to-noise (MRSN) ratio was calculated and the optimum combination level of factors was obtained simultaneously using Taguchi’s parametric design. Among the three, the most influencing factor for the chosen objective was found out by analyzing the MRSN ratio through ANOVA. The optimum combination obtained shows a lower NOx emission with less influence on smoke density and brake thermal efficiency.