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Teaching computational thinking (CT) skills entails not only learning the syntax and commands of a programming language but are also developing higher-order skills that are essential for students’ future careers. To address this challenge, this study proposed a pedagogical method that combined project-based learning (PBL) and self-regulated learning (SRL) to train students in CT in a computer programming course. Guided by the higher-order CT framework, this study adopted a pre- and post-test quasi-experimental research design. A total of 173 college students from three computer programming classes participated in this study. Overall, the findings suggested that the integrated method could effectively promote CT among novice students through programming. And further research was recommended to improve the proposed pedagogical method.