The outbreak of pandemics such as COVID‐19 can result in cascading effects for global systemic risk. To combat an ongoing pandemic, governmental resources are largely allocated toward supporting the health of the public and economy. This shift in attention can lead to security vulnerabilities which are exploited by terrorists. In view of this, counterterrorism during a pandemic is of critical interest to the safety and well‐being of the global society. Most notably, the population flows among potential targets are likely to change in conjunction with the trend of the health crisis, which leads to fluctuations in target valuations. In this situation, a new challenge for the defender is to optimally allocate his/her resources among targets that have changing valuations, where his/her intention is to minimize the expected losses from potential terrorist attacks. In order to deal with this challenge, in this paper, we first develop a defender–attacker game in sequential form, where the target valuations can change as a result of the pandemic. Then we analyze the effects of a pandemic on counterterrorism resource allocation from the perspective of dynamic target valuations. Finally, we provide some examples to display the theoretical results, and present a case study to illustrate the usability of our proposed model during a pandemic.