Misconceptions about engineering and science concepts persist among engineering students, and some are resistant even to direct instruction. This paper reports on a unique form of computer-based online learning module, designed to help engineering undergraduates learn difficult concepts in the thermal and transport sciences (specifically, heat transfer, mass diffusion, and microfluidics). The design of these modules has been informed by relevant research on cognitive psychology and technology-enhanced learning. Specifically, the modules are based on the prior work of Chi and Slotta, which focuses on helping students understand the emergent properties of complex physical systems, thereby providing a means for promoting conceptual change within these challenging domains. The modules were designed and hosted in a Web-based learning management system, where a variety of interactive materials and inquiry prompts were incorporated to help students better understand the concepts and visualize the phenomena. Engineering students’ perceptions of computer-based online learning are reported along with learning outcomes that resulted from their use of the modules. This was the first study to provide a discipline-based example in engineering education for how to use computer-based online learning and emergent properties of complex systems to help undergraduate engineering students learn difficult concepts. It has implications for (1) designing effective online learning environments to help students learn difficult science and engineering concepts; and (2) developing effective instructional strategies for promoting conceptual change.