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Purpose: In a boundary layer ingestion (BLI) propulsion system, the fan operates continuously under distorted inflow conditions, leading to an increment of aerodynamic loss and in turn impacting the potential fuel burn reduction of the aircraft. Usually, in the preliminary design stage of a BLI propulsion system, it is essential to assess the impact of fuselage boundary layer fluids on fan aerodynamic performances under various flight conditions. However, the hub region flow loss is one of the major loss sources in a fan and would greatly influence the fan performances. Moreover, the inflow distortion also results in a complex and highly nonlinear mapping relation between loss and local physical parameters. It will diminish the prediction accuracy of the commonly used low-fidelity computational approaches which often incorporate traditional physics-based loss models, reducing the reliability of these approaches in evaluating fan performances. Meanwhile, the high-fidelity full-annulus unsteady Reynolds-averaged Navier–Stokes (URANS) approach, even though it can give rather accurate loss predictions, is extremely time-consuming. This study aims to develop a fast and accurate hub loss prediction method for a BLI fan under distorted inflow conditions. Design/methodology/approach: This paper develops a data-driven hub loss prediction method for a BLI fan under distorted inflows. To improve the prediction accuracy and applicability, physical understandings of hub flow features are integrated into the modeling process. Then, the key physical parameters related to flow loss are screened by conducting a sensitivity analysis of influencing parameters. Next, a quasi-steady assumption of flow is made to generate a training sample database, reducing the computational time by acquiring one single sample from the highly time-consuming full-annulus URANS approach to a cost-efficient single-blade-passage approach. Finally, a radial basis function neural network is used to establish a surrogate model that correlates the input parameters and the output loss. Findings: The data-driven hub loss model shows higher prediction accuracy than the traditional physics-based loss models. It can accurately capture the circumferentially and radially nonuniform variation trends of the losses and the associated absolute magnitudes in a BLI fan under different blade load, inlet distortion intensity and rotating speed conditions. Compared with the high-fidelity full-annulus URANS results, the averaged relative prediction errors of the data-driven hub loss model are kept less than 10%. Originality/value: The originality of this paper lies in developing a new method for predicting flow loss in a BLI fan rotor blade hub region. This method offers higher prediction accuracy than the traditional loss models and lower computational time cost than the full-annulus URANS approach, which could realize fast evaluations of fan aerodynamic performances and provide technical support for designing high-performance BLI fans. [ABSTRACT FROM AUTHOR]