The United States Department of Defense (DoD) Strategic Capabilities Office initiated Project Pele, with the primary goal of designing, constructing, and demonstrating a prototype mobile microreactor within the next 5 years. A key consideration in deploying microreactors is the associated risks incurred during transportation. This work presents an integrated probabilistic risk assessment methodology to quantitatively assess the risks associated with the transportation of microreactors. The resulting risk insights support decision-making in the early stages of design and transportation route planning. A case study, based on a domestic route from Idaho National Laboratory to the Port of New Orleans, demonstrates that the risks associated with transporting a microreactor are well within established regulatory limits and are comparable to annual effective doses from background radiation. In this analysis, maritime transportation exhibited the lowest risk, followed by rail and then highway.