This paper highlights a risk-based decision-making framework on a basis of probabilistic risk assessment (PRA). Its aim is to enable stakeholders of transport infrastructures to systematically and effectively allocate their limited resources and consequently improve resilience when facing the potential risk of a terrorist attack. The potential risk of a terrorist attack affects the inter-operation of transportation infrastructures including airports and rail stations, the regional economy, and imposes additional costs of security or any countermeasures. This novel framework is thus established in order to model the security system, to consider a multitude of threat scenarios, and to assess the decisions and choices taken by the aggressors during various stages of their attack. The framework has capability to identify the state of partial neutralization, which reveals the losses incurred when the terrorist could not reach the primary target. In this study, an underground railway station interconnected to an international airport has been used as a case study to demonstrate the effectiveness of this novel framework. By the rigorous assessment of potential losses during a variety of threat scenarios, four countermeasures that could minimise losses are proposed: screening of passengers by observation techniques (SPOT), a surveillance system, increase of the cargo screening rate, and blast-resistant cargo containers. The cost and efficiency assessment is employed to determine the most suitable countermeasures when the value of the security measures equal their cost. Note that ongoing research is still needed to establish better countermeasures since there is no end to the creativity of terrorists. The new technology, such as wireless sensors, will play an important role in the security system in the future. In particular, this study will help insurance and rail industries to model and manage risk profiles at critical infrastructure.