The study examined the effect of teaching text-based programming with a physical programming tool on secondary school students' computational thinking skills and self-efficacy perceptions. The study was conducted according to a sequential explanatory design as a mixed method research. The study group consisted of 85 secondary school students. Within the scope of the study, a physical programming tool called Micro:bit was used to teach Python programming for a period of 6 weeks. Data were collected using the Self-Efficacy Perception Scale for Computational Thinking Skill, Bebras: International Challenge on Informatics and Computational Thinking Tasks, tests focused on programming tool, concepts, and processes, and through semi-structured interview questioning. According to the findings obtained from pretests and posttests, a significant and positive difference was found in the students' computational thinking skills and self-efficacy perceptions towards computational thinking skill. As a result of having received instruction in programming, the students satisfactorily learnt the required programming concepts and processes. Through learning Python programming with a physical programming tool, the students not only gained the skills required to write appropriate syntax, and to test and debug code, but they also learnt programming concepts such as variables, conditional expressions, loops, and functions.