In medical training, allowing learners to take pauses during tasks is known to enhance performance. Cognitive load theory assumes that insertion of pauses positively affects cognitive load, thereby enhancing performance. However, empirical studies on how allowing and taking pauses affects cognitive load and performance in dynamic task environments are scarce. We investigated the pause effect, using a computerized simulation game in emergency medicine. Medical students (N = 70) were randomly assigned to one of two conditions: simulation with (n = 40) and without (n = 30) the option to take pauses. All participants played the same two scenarios, during which game logs and eye-tracking data were recorded. Overall, both cognitive load and performance were higher in the condition with pauses than in the one without. The act of pausing, however, temporarily lowered cognitive load, especially during intense moments. Two different manifestations of the pause effect were identified: (1) by stimulating additional cognitive and meta-cognitive processes, pauses increased overall cognitive load; and (2) through relaxation, the act of pausing temporarily decreased heightened cognitive load. Consequently, our results suggest that in order to enhance students’ performance and learning it is important that we encourage them to utilize the different effects of pausing.