Inter-shaft fuel supply systems (ISFSSs) consisting of a shaft annulus and a fuel slinger are usually used in micro turbojet engines to pump the fuel to the combustor, aiming at reducing engine's size and weight. Differing from the configuration with stationary fuel pipework, the fast-rotating shaft in the annulus would induce significant drag jeopardizing the fuel supply during engine acceleration. This study investigates the flow physics inside a micro turbojet engine ISFSS. Air–fuel two-phase flow is found in the slinger cavity and the shaft annulus, with main gas path air ingress into the ISFSS under disk pumping of the slinger, and the ingress is enhanced by introducing blades on the slinger disk. Results show that the axial flow drag in the shaft annulus is reduced as air being ingested in. Further investigation indicates that the best supplied fuel volume fraction is 0.8, and this can reduce the axial drag in the shaft annulus by ∼63%, compared with the single-phase fuel flow. Therefore, two-phase air–fuel mixture is proposed for the ISFSS drag reduction.