Fuel cell systems for heavy-duty applications typically consist of multiple modules that can supply power jointly or individually. This work presents a novel energy management concept for the health-conscious activation of multi-module fuel cell systems to mitigate degradation in short or low-demanding driving cycles. The proposed activation strategy contributes to developing intelligent control systems for fuel cell electric trucks that optimally decide between battery-only, one-module, or two-module operation depending on the expected driving scenarios. The strategy derives from an optimal energy management problem formulation solved using dynamic programming, considering factors such as truckload, initial battery charge, route elevation, and trip length. Activation strategies for multi-module fuel cell systems are of significant interest because fuel cell degradation is severely affected by start-up/shut-down cycles. This type of degradation is dominant in urban or rural driving cycles because they are significantly shorter than motorway ones. By avoiding start-up/shut-down cycles in short and low-demanding driving scenarios, the proposed strategy significantly reduces the overall number of cycles over the fuel cell lifetime, mitigating degradation. In conclusion, this paper presents an innovative solution to improve the durability of fuel cell powertrains, which is still a significant barrier to their market penetration and advancement in automotive applications. In particular, the activation strategy contributes to developing intelligent control systems for fuel cell electric trucks, which can optimally decide the number of active fuel cell modules depending on the driving scenario, ultimately leading to more durable fuel cell systems.