This paper presents a newly developed methodology for multipoint aerodynamic design of ultra-short nacelles for ultra-high bypass ratio turbofan engines. An integrated aerodynamic framework, based on parametric geometry generation and flow field solution via three-dimensional Reynolds-Averaged Navier-Stokes equations, was built and used for designing several ultra-short nacelle shapes and to evaluate their aerodynamic performance. An approach for estimating the static pressure distribution at the fan face, based on the parallel compressor theory, is presented and validated. A design strategy is introduced and various test cases are evaluated under the following critical operating conditions: mid-cruise, low speed/ high angle of attack, and pure crosswind. The major design parameters are highlighted and their influence in the flow field is discussed in detail for all the chosen flight conditions. Performance was evaluated by assessing inlet flow distortion and by bookkeeping of thrust and drag. The framework has proven to be suitable for designing high performance nacelles capable of operating under critical flight conditions, without flow separation or high levels of distortion. Drooping the inlet by 4 degrees is shown to reduce the drag at cruise by 1.9%, which also has a large beneficial impact on internal lip separation at high incidence conditions. Furthermore, crosswind was identified as the most severe of the conditions, requiring a drastic reshaping of the nacelle to avoid internal lip separation. Two final nacelle designs were compared: the first allowing inlet separation under a 90-degree crosswind condition, whilst the second was reshaped to be separation-free under all operating conditions. Reshaping to avoid separation