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Background: Previous work has identified that the benefits of learning with videogames and learning from simulations. However, recent meta‐analytic work has also identified that little research directly compares learning with videogames and learning with simulations. Objectives: This study examines two learning technologies and their corresponding pedagogical approaches and compares them for learning the Science, Technology, Engineering and Mathematics topic of electric charges. Methods: Participants were randomly assigned to either an intervention using a computer simulation for inquiry‐based learning or a computer videogame for game‐based learning. Their learning gains, self‐reported emotional state and experienced cognitive load were recorded. Results: We found that both learning environments improved conceptual learning, and there were no statistically significant differences between the two conditions. Participants did perceive the game‐based environment to be more engaging as well as more frustrating. We also found that cognitive load did not predict learning—however, different types of cognitive load correlated with different emotions. Overall, participants in both conditions were engaged and perceived understanding of the topic, yet they also experienced both confusion and task‐unrelated thoughts. Takeaways: When learning with simulations and videogames, educators need to align intended learning outcomes with pedagogical approaches enabled by technology. In addition, a balance between principles of multimedia learning to reduce or prevent extraneous processing, and scaffolding to reduce negative effects of learning with technology, need to be considered. Lay Description: What is already known about this topic: Research on the use of computer simulations for learning has identified positive learning effects regarding achievement outcomes, inquiry skills and noncognitive outcomes.Research on the use of videogames for learning has suggested learning benefits, such as improved working memory, development of creativity skills and achievement outcomes.Recent meta‐analytic work has identified that there is little research that directly compares learning with videogames and learning with simulations. What this paper adds: Learning benefits of difficult Science, Technology, Engineering and Mathematics (STEM) concepts may be different for game‐based learning (GBL) than inquiry‐based learning (IBL).Positive emotions can be experienced when learning via GBL than when learning via IBL.Students, who experience more positive emotions may also achieve higher learning gains.Students' cognitive load may be different when learning with GBL than when learning via IBL.Students experiencing high cognitive load (i.e., intrinsic and extraneous) may show lower learning gains.Students experiencing high cognitive load (i.e., intrinsic and extraneous) may show higher level of mind‐wandering, frustration, or confusion. Implications for practice and/or policy: Learning with simulated inquiry base environment and game base environment improved conceptual learning.GBL was more engaging and more frustrating for students, when learning with computer videogames.Cognitive load did not predict STEM learning with technologies.Different cognitive load correlated with different learning emotions. [ABSTRACT FROM AUTHOR]