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BACKGROUND While the surface registration technique has the advantage of being relatively safe and the operation time is short, it generally has the disadvantage of low accuracy. PURPOSE This research proposes automated machine learning (AutoML)-based surface registration to improve the accuracy of image-guided surgical navigation systems. METHODS The state-of-the-art surface registration concept is that first, using a neural network model, a new point-cloud that matches the facial information acquired by a passive probe of an optical tracking system (OTS) is extracted from the facial information obtained by computerized tomography (CT). Target registration error (TRE) representing the accuracy of surface registration is then calculated by applying the iterative closest point (ICP) algorithm to the newly extracted point-cloud and OTS information. In this process, the hyperparameters used in the neural network model and ICP algorithm are automatically optimized using Bayesian Optimization with Expected Improvement to yield improved registration accuracy. RESULTS Using the proposed surface registration methodology, the average TRE for the targets located in the sinus space and nasal cavity of the soft phantoms is (0.939 ± 0.375) mm, which shows 57.8 % improvement compared to the average TRE of (2.227 ± 0.193) mm calculated by the conventional surface registration method (p < 0.01). The performance of the proposed methodology is evaluated, and the average TREs computed by the proposed methodology and the conventional method are (0.767 ± 0.132) mm and (2.615 ± 0.378) mm, respectively. Additionally, for one healthy adult, the clinical applicability of the AutoML-based surface registration is also presented. CONCLUSION Our findings showed that the registration accuracy could be improved while maintaining the advantages of the surface registration technique. This article is protected by copyright. All rights reserved.