The impact of digitalization on the maritime industry is increasing day by day. In this sense, realistic engine room simulators (ERS), which fulfill the requirements of the International Maritime Organization, are getting more important and frequently used in the field of maritime education and training. Besides, it is observed that there is an increase in ERS usage in experimental academic studies because opportunities for realizing critical and risky operations on real marine vessels in the ERS and determining the effects of failures through simulations encourage researchers. However, there is uncertainty about the method followed in ERS-based studies since the use of the ERS varies at the discretion of each author. In this study, a novel methodology is proposed to eliminate the uncertainty and provide standardization of engine simulators as a tool in academic studies. Real ship machinery operations, simulator specifications, scientific methods, instructor and operator interventions are utilized in this methodology framework. To prove the effectiveness of the methodology, a two-stroke MAN B&W 6S50 MC-C marine diesel engine turbocharger (TC) exhaust side fouling effects are analyzed. In addition, the validation of the application conducted by the proposed methodology is carried out by consulting experts with marine experience during the design and evaluation of the application. Thus, it is aimed to obtain more realistic and reliable data through a systematically designed simulation process.