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Inverse heat transfer (IHT) techniques are often used to reconstruct the surface heating conditions on spacecraft thermal protection systems (TPS) during atmospheric entry. Current IHT techniques for entry spacecraft applications, however, demand substantial computational resources, and are impractical for analyses such as uncertainty quantification and real-time health monitoring. In this paper, a Green’s function sensor fusion approach is used to reconstruct the TPS surface aeroheating conditions on experimental spaceflight and ground test systems from collocated temperature and heat flux sensors embedded in the TPS. The algorithm leverages Green’s functions to model the heat conduction within the spacecraft TPS and stabilizes the recovery of the surface heating condition using the direct heat flux sensor measurement. The algorithm is validated using arc-jet ground test data and applied to the reconstruction of the Mars 2020 backshell heating during Martian atmospheric entry. The performance of the algorithm is benchmarked against a current state-of-the-art IHT framework, FIAT_Opt. The Green’s function-based reconstruction algorithm recovers the net hot-wall heat flux absorbed by the TPS and the incident heat flux from the atmospheric entry environment in close agreement with FIAT_Opt. Notably, computation of the surface heating condition is completed in three orders of magnitude less time with the Green’s function sensor fusion approach using a consumer-grade PC, versus with FIAT_Opt running on a high performance computer cluster. The efficiency of the algorithm is leveraged to compute the uncertainty contributions of input parameters to the total uncertainty in reconstructed Mars 2020 backshell heating for the full atmospheric entry heat pulse. The sensitivity analysis uncovers that, at different times throughout the entry heat pulse, uncertainties in the TPS specific heat, thermal conductivity, and emissivity are all dominant drivers of the reconstruction uncertainty. These results demonstrate Green’s functions and sensor-fusion techniques as promising IHT approaches to reconstruct atmospheric entry environments from TPS-embedded measurements, and highlight how these techniques may give access to post-flight analyses previously hindered by the prohibitive cost of current methods.