Programming skills (PS) refer to coding and debugging that are required for those who write a program in any programming language. Coding can be described as the implementation aspect of programming, whereas debugging can broadly be defined as fixing any incorrect code that is found after running the programming test. Higher-order thinking skills (HOTs) refer to the top three levels of Bloom’s taxonomy which are Analysis, Synthesis, and Evaluation. This study aims to determine the relationship between PS and HOTs among secondary students. Many studies indicate that students who attend programming courses for first time have low levels of performance in PS. Coding and debugging skills reflect higher-order thinking levels. Therefore, an objective of this study was to investigate the effect of coding and debugging skills on their HOTs. The benefits of having PS among learners are that they are able to achieve HOTs. Indeed, these relationships may be explained by programmers need to apply all these HOTs throughout the three phases of the programming process. Students who have low levels of PS are able to achieve the analysis level, while students who have moderate levels of PS able to achieve the synthesis level, and finally, students with high levels of PS are able to achieve the evaluation level.