Recently, design thinking has become recognized as a necessity for every student, especially when they engage in design-based learning, as a pedagogical approach to science, technology, engineering, and mathematics education. However, design-based learning is mostly based on forward engineering, in which students’ design thinking can be nurtured by designing unknown solutions. Little is known about whether design thinking can be facilitated in the context of reverse engineering, when students learn from already designed products. This study therefore seeks to explore the perceptions of 38 ninth-grade students on the characteristics of design thinking before and after a four-week reverse engineering project, using Likert scales to measure six aspects of design thinking, namely (a) being comfortable with uncertainty and risks, (b) human-centeredness, (c) mindfulness to the process and impacts on others, (d) collaboratively working with diversity, (e) orientation to learning by making and testing, and (f) being confident and optimistic to use creativity. The data were analyzed using descriptive and inferential statistics, including means, standard deviations, paired-samples t-tests, and Wilcoxon signed-rank tests. The results indicate that two aspects, human-centeredness and being confident and optimistic to use creativity, were significant ( p = 0.008 and p = 0.043, respectively), with size effects of 0.43 and 0.34, respectively. Based on this potential, reverse engineering can be a design-based learning approach to facilitate students’ design thinking. It is recommended that instructional activities involving reverse engineering maintain some degree of ambiguity and risk to prevent design fixation among students.