How do students apply systems thinking to make sense of a computational model of crowd evacuation? We developed a participatory simulation in which users play the role of evacuees that move through a narrow passageway. This simulation demonstrates that when exceeding a certain speed, moving through narrow bottlenecks, is more likely to create clogs, leading to a slower passing rate. The participatory simulation was introduced in a lesson about school evacuation in a group of 9th graders. Their explanations of crowd evacuation, were compared to a similar group of 9th graders who learned the same ideas in a lecture without using the simulation. We found that using the simulation did not improve students’ system thinking about crowd evacuation compared to lecture-based instruction. About 80% of the students in both groups suggested partial/incomplete explanations of the inverse relationship between the desire to move faster as individuals and the opposite consequence of slower evacuation. Interviews with students revealed that some of them perceived the simulation scenario to be different from the organized and coordinated evacuation drills that they partook. Others, were engrossed in their own experiences as evacuees, that obscured their ability to relate the motion of individual evacuees and the overall evacuation rate of the crowd. In a second study, we examined whether prior learning of a different emergent process (spread of a disease) with a computational model, can prepare students for learning the counterintuitive phenomenon of crowd evacuation. We found that introducing a participatory simulation of the spread of a disease in a different group of 9th graders, increased their appreciation of the evacuation simulation as a learning tool, and consequently–their explanations. We conclude that computational models have the potential to enhance systems thinking, but their affordances depend on prior preparation for learning with other complex systems models.