Background Being easy to learn and fun, block‐based programming tools are widely used to teach students introductory programming. Scratch and LEGO robots are two popular block‐based programming tools. However, the objects they manipulate are completely different. Scratch manipulates graphical virtual sprites, whereas LEGO robots manipulate physical robots. Different manipulating objects may bring students varied learning experiences. Objectives This study compared undergraduate students' learning engagement and flow experience when programming on Scratch and LEGO robots. Methods The study was conducted in a programming course which involved 28 Chinese undergraduates. At the end of the 14‐week course, all students were requested to complete the questionnaire twice, one for their perceptions of Scratch and the other for those of LEGO robotics. Three semi‐structured focus‐group interviews were also conducted for students' perceptions of the course. Results and Conclusions The results showed that LEGO robots scored significantly higher on behavioural and emotional engagement, while cognitive engagement was not significantly different. As for the flow experience, Scratch provided students with a greater sense of control, while LEGO robots allowed students to experience temporal distortion. There were no significant differences in terms of clear goals and immediate feedback. Takeaways Our study contributes to a better understanding of students' engagement and flow experience in block‐based programming and helps teachers select appropriate programming tools for teaching.