This study introduces a quantum game-theoretic framework to model strategic interactions in a two-echelon deteriorating supply chain under uncertainty. By treating the deterioration rate as a stochastic variable and incorporating quantum entanglement, the proposed model captures interdependencies often ignored in classical Nash and Stackelberg games. Comparative analyses demonstrate that quantum structures enhance profitability, coordination, and robustness to fluctuations and risk aversion. A mean–variance utility assessment further validates the quantum model’s superiority, highlighting its promise for managing fragile, time-sensitive supply chains.