This paper deals with the pricing and allocation problems that arise in a mobility permit (MP)-based traffic management system on single bottleneck roadways. We present a permit endowment (pricing and allocation) mechanism and address the efficiency of such a system in mitigating the congestion at bottlenecks under users’ preferences and incomplete information setting. To perform an efficient permit allocation, we develop a mixed-integer programming (MIP) optimization model restrained by user priority and MP availability constraints. For the pricing problem, we present an iterative auction mechanism on top of the MIP-based permit allocation module. We present a performance comparison of the presented mechanism against hypothetical coordinated and centralized efficiency-oriented and equity-oriented systems. Computational results show the potential of the proposed pricing and allocation mechanism for managing MPs in a network with a single-bottleneck roadway where the mobility users, mobility service provider, and system regulator’s concerns must be integrated into a MP-based traffic congestion management solution.