Gas turbine fuel burn for an aircraft engine can be obtained analytically using thermodynamic cycle analysis. For large-diameter ultra-high bypass ratio turbofans, the impact of nacelle drag and propulsion system integration must be accounted for in order to obtain realistic estimates of the installed specific fuel consumption. However, simplified models cannot fully represent the complexity of installation effects. In this paper, we present a method that combines thermodynamic cycle analysis with detailed Computational Fluid Dynamics (CFD) modelling of the installation aerodynamics to obtain the fuel consumption at a given mission point. The flow field and propulsive forces arising in a transport aircraft powered by an ultra-high bypass ratio turbofan at cruise are first examined to characterise the operating conditions and measure the sensitivity to variations of the incidence at transonic flight. The proposed methodology, in which dynamic balance of the vehicle is achieved at each integration point, is then applied along a cruise segment to calculate the cumulative fuel burn and the change in the specific fuel consumption.