The transonic aerodynamics of an advanced, over-the-wing nacelle, subsonic transport configuration are assessed using both Euler and Navier-Stokes computational fluid dynamics and results are compared to a similar configuration with an under-the-wing nacelle installation and a similar wing-body configuration. The over-the-wing nacelle configuration is designed with a novel inboard wing channel section between the nacelle and the fuselage that produces favorable aerodynamic interference and reduces the overall drag. Qualitative observations and quantitative drag computations are performed for the three configurations at a cruise Mach number of 0.78. It was found that, at the cruise point, the inboard wing channel section of the over-the-wing nacelle configuration effectively produces a favorable pressure distribution but that the overall drag, compared to the under-the-wing nacelle configuration, is higher. This excess drag, however, was found to be largely localized in the nacelle interior. Euler and Navier-Stokes computational fluid dynamics solutions were obtained for additional Mach numbers to assess the transonic drag-rise characteristics. The computational fluid dynamics solutions showed that the over-the-wing nacelle configuration has higher drag at lower Mach numbers than the under-the-wing nacelle configuration but experiences a milder overall drag rise and has lower drag at higher Mach numbers.