Design of the intake system of an internal combustion (IC) engine is one of the critical parameters to improve the performance of an engine. Induction pressure waves (compression and rarefaction waves) are created in the intake runner due to valve operations. If the intake runner is tuned correctly, a compression wave can boost the intake air flow improving the volumetric efficiency which increases the torque and power of the engine. In this research, the intake runner diameter and valve timing were varied individually, after which both were varied together to achieve optimum volumetric efficiency. A single-cylinder, four-stroke spark-ignited 510 cc naturally aspirated engine was used for the analysis. Simulations were carried out using engine simulation software Ricardo Wave to find the effect of intake runner diameter and timing on the engine performance. A chassis-dyno test was made on the engine to know its factory state performance and compared the torque and power with the simulation data. As a result, the validated model is found to have a deviation of around 10.0% from the actual chassis dyno test. Gains achieved upon combined effects of variation of both intake runner diameter and intake valve timing across the engine speed range were appreciable. It was observed that when only the runner diameter was varied, the improvement in volumetric efficiency was approximately 8.5%. Similarly, when only the valve timing was varied, around 3% improvement was seen. However, upon varying both the intake runner diameter and intake valve timing for each speed simultaneously, an average increment of 12% was noted.