Heat and temperature concepts are found at all levels in the science curricula and are well-known for creating conceptual difficulties for learners. Students have difficulty understanding concepts related to heat, temperature, and thermal radiation. Inquiry-based pedagogies that can foster the learning of these difficult concepts are needed. Physical experiments and computer simulations are two alternatives with the potential to increase students' conceptual understanding. The purpose of this study is to compare the effectiveness of computer simulations with primarily physical experiments on undergraduate engineering students' understanding of rate versus amount and thermal radiation concepts. While some previous research has found that students using computer simulations outperformed those doing physical experiments, other research has discovered no significant differences in the conceptual understanding of students using the two different pedagogies. Given these findings, more research is warranted. A secondary purpose of this study is to determine whether computer simulations and physical experiments would be equally effective with different heat transfer concepts and by gender. Is there a difference in the students' level of understanding of rate versus amount of heat transferred and thermal radiation by method of instruction? Does one pedagogy work better for one concept? Does the effectiveness of the modes of instruction vary by gender? This quasi-experimental study compared two implementation methods for inquiry-based activities. One group of participants used computer simulations while the other group primarily did physical experiments. Descriptive statistics showed that while students' scores on the pre-test were very close, there was a difference between them on the post-test favoring those taught by doing a physical experiment.