Engine noise, as a source of sound pollution for humans and the environment, can be reduced by designing a high-performance muffler. This study presents a novel, organized design process of that muffler for the KTM390 engine as a case study. The acoustic simulation analysis is performed in COMSOL software and aerodynamic analysis is performed in ANSYS Fluent. The features of the muffler considered in this designing process are the overall length of the muffler, the presence of baffles and related parameters (baffle distance, baffle hole diameter, and baffle hole offset), and the effects of extended tubes. In order to evaluate the acoustic performance of the muffler, an objective function has been defined and measured on two frequency ranges, 75–300 Hz and 300–1500 Hz. For evaluating the aerodynamic performance of that, the amount of backpressure is analyzed to achieve a maximum of 3.3 kilopascals for this muffler. The selection of the appropriate parameters includes comparing the resulting transmission loss curves and quantitative evaluation of objective functions (for transmission loss) and backpressure. This organized design process (i.e., tree diagram) leads to an increase in the efficiency of designing mufflers (for example, 41.2% improvement on backpressure).