Autonomous/self-driving vehicles have gained significant attention these days, as one of the intelligent transportation systems. However, those vehicles have risks related to their physical implementation and security against cyber threats. Therefore, this study proposes a new security-by-design model for estimating the uncertainty of autonomous vehicles and measuring cyber risks; thus it assists decision-makers in addressing the risks of the physical design and their attack surfaces. The proposed model is developed using neutrosophic sets that efficiently tackle multi-criteria decision-making (MCDM) problems with extensive conflicting criteria and alternatives. The proposed model integrates MCDM, Analytic Hierarchy Process (AHP), Multi-Attributive Border Approximation Area Comparison (MABAC), and Preference Ranking Organization Method for Enrichment Evaluations II (PROMETHEE II), along with single-valued neutrosophic sets (SVNSs). An illustrative case considering ten risks in self-driving vehicles is used to validate the feasibility of the proposed model. Compared to the state-of-the-art methods, the proposed model is considered consistent and reliable to deal with and represent uncertainty and incomplete risk information using neutrosophic sets.