Researchers have indicated that the collaborative problem‐solving space afforded by the collaborative systems significantly impact the problem‐solving process. However, recent investigations into collaborative simulations, which allow a group of students to jointly manipulate a problem in a shared problem space, have yielded divergent results regarding their effects on collaborative learning. Hence, this study analysed how students solved a physics problem using individual‐based and collaborative simulations to understand their effects on science learning. Multiple data sources including group discourse, problem‐solving activities, learning test scores, and questionnaire feedback were analysed. Lag sequential analysis on the data found that students using the two simulations collaborated with peers to solve the problem in significantly different patterns. The students using the collaborative simulations demonstrated active engagement in the collaborative activity; however, they did not transform discussions into workable problem‐solving activities. The students using the individual‐based simulation showed a lower level of collaboration engagement, starting with individual exploration of the problem with the simulation, followed by group reflection. The two groups also showed significant differences in their learning test scores. The findings and pedagogical suggestions are discussed in the hope of addressing critical activity design issues in using computer simulations for facilitating collaborative learning. Lay Description What is currently known about the subject matter? Students tend to solve problems with simulations individually rather than collaboratively. The free‐riding effect impedes student engagement in the collaborative process. Collaborative simulations offer new affordances to better facilitate CPS processes. What their paper adds to this? Collaborative simulations strengthen interdependence and engagement in collaboration. However, students did not show a significant enhancement in the learning tests. They had difficulties transforming discussions into workable problem‐solving actions. What the implications of study findings for practitioners? Collaborative simulations can be applied to enhance collaborative engagement. CPS activities should carefully leverage individual and collaborative learning. Prompts that help students to closely relate their discussion to the simulation are needed.