While course videos are powerful teaching resources in online courses, students often have difficulty sustaining their attention while watching videos and comprehending the content. This study adopted teacher annotations on videos as an instructional support to engage students in watching course videos. Forty-two students in an undergraduate course at a university in Taiwan were randomly divided into a control group that watched a course video without teacher annotations, and an experimental group that watched a course video with teacher annotations. The collected data included a learning engagement survey, students’ video watching behaviors, and student interviews. The results showed that there were differences in student learning engagement between the control and experimental groups. The teacher annotations increased students’ behavioral and cognitive engagement in watching the video but did not increase their emotional engagement. In addition, this study identified how students learned when watching the course video with the teacher annotations through highlights of the video content, literal questions, reflective questions and inferential questions. The results concluded that teacher annotations and student learning engagement were positively correlated. The students acknowledged that their retention and comprehension of the video content increased with the support of the teacher annotations.