A CFD simulation of the flow within a motored two-port loop-scavenged two-stroke engine is described. The simulation is carried out using the STAR-CD CFD code and employs a multi-block approach to simulate the flow within the transfer duct, cylinder, and exhaust duct. A moving mesh with cell layer activation-deactivation is used to represent the reciprocating piston motion. Predictions of the flow within the cylinder and at the transfer port are presented over the open cycle and are compared to an existing measured velocity field for an engine speed of 600 rpm and a delivery ratio of unity. The results show the in-cylinder flow to have a highly complex structure dominated by recirculating flow features. The in-cylinder flow is considerably affected by reverse flow through the exhaust port at exhaust port opening, and is not seen to fully establish until after bottom dead centre. In comparison to the measured flow, the global flow properties and large scale flow structures are well predicted, with detailed flow being less accurately replicated. A good correlation between measured and predicted velocity fields is achieved by exhaust port closure. Predicted transfer port efflux correlates well with the measured efflux until port opening rises to 90% of full port opening, after which the flow separation that occurs within the transfer duct is not well predicted. Accuracy of port efflux prediction improves again as the measured flow re-attaches within the duct.