Compressed natural gas (CNG's) lower gas jet momentum during a low load operation creates a non-uniform air-fuel mixture that affects ignition and combustion quality. Direct injection of CNG with optimum injection timing is expected to improve volumetric efficiency, ignition quality, and combustion process. A comparative study on the effect of end-of-injection (EOI) timing on volumetric efficiency, thermal efficiency, combustion duration, and emissions were carried out for PFI gasoline, PFI CNG, and DI CNG engine. Experimental results indicate that the PFI CNG engine is more influential in EOI timing than gasoline engines. The performance of the PFI CNG engine is improved when the injection occurs during the intake valve open period compared to the closed valve period with higher thermal efficiency, volumetric efficiency, and IMEP. A shorter flame development angle and combustion duration were observed when EOI timing was in the open intake valve condition. DI CNG improved volumetric efficiency at advanced EOI timing compared to the PFI CNG engine. However, the combustion process is critically dependent on injection timing and air-fuel mixing duration. A CFD investigation was carried out to visualize the importance of in-cylinder mixing in the combustion process. An excess advanced and retarded EOI resulted in turbulent kinetic energy loss resulting in diluted and highly stratified mixture formation at the spark plug location. Thus, optimum EOI timing provided an optimum environment to initiate the spark and flame growth. An advanced EOI timing is required for increasing throttle and engine speed.