To reduce fuel-burn and emissions, there is a drive toward higher bypass ratio and smaller high-pressure ratio core engines. This makes the design of the ducts connecting compressor spools more challenging as the higher radius change increases aerodynamic loading. This is exacerbated at inlet to the engine core by fan root flow which is characterized by a hub-low-pressure profile and large secondary flow structures. Additionally, shorter, lighter nacelles mean that the intake may not provide a uniform inlet flow when the aircraft is at an angle of attack or subject to cross winds. Such inlet distortion can further degrade the flow entering the engine. A combination of experiments and computational fluid dynamics (CFD) has been used to examine the effects on the aerodynamics of an engine section splitter (ESS) and transition duct designed to feed the low-pressure spool of a high bypass ratio turbofan. A test facility incorporating a 1½ stage axial compressor was used to compare system performance for a flat rotor exit profile to one with a hub deficient flow. Validated Reynolds averaged Navier–Stokes (RANS) CFD was then used to further investigate the effects of increased inlet boundary layer thickness and bulk swirl distortion at rotor inlet. These changes were seen to have a surprisingly small effect on the flow at the duct exit. However, increased secondary flows were observed which degraded the performance of the ESS and significantly increased loss. Nevertheless, the enhanced mixing delayed separation in the duct suggesting that overall the design was reasonably robust albeit with increased system loss.