The transient, three-dimensional scavenging flow inside a novel two-stroke engine has been investigated both experimentally in a scaled water model as well as numerically using a commercial CFD code incorporating an unsteady Reynolds averaged Navier–Stokes (URANS) formulation. The scavenging flow consists of 16 round jets in close proximity of each other and the cylinder wall, developing from the top of the combustion chamber down towards the exhaust ports located along the wall at the bottom of the cylinder. Flow visualization of the scavenging flow was performed using a scaled fixed-piston water model and was used as a means of validating the URANS simulations themselves. The flow visualization experiments provided insight into the complex jet–jet and jet–wall interactions within the engine cylinder. These interactions were not as well predicted by the CFD simulations. In fact, the CFD simulations were found to significantly under-predict the turbulent mixing between the jets. This suggests that unsteady-RANS formulations are incapable of reproducing the large-scale and unsteady mixing structures associated with the vortex shedding between the closely-spaced jets.