Flipped Classroom (FC) has become an increasingly popular model in many disciplines in today's educational system. In order for the FC model to be effective, it is important for the student to have self-regulation skills. It is especially important that students have advanced self-regulatory skills so that the online learning process of the FC model can be successfully completed. It is believed that the metacognitive support (MS) provided by the pedagogical agent during the online process of the FC model will contribute to the development of self-regulation skills of the students. The purpose of this research is to examine the impact of MS via pedagogical agent in the FC model on students' self-regulation skills. The research was carried out according to experimental design, and the participants of the research consist of 102 university students. The data of the study were collected using self-regulated learning scale. As a result of the research, it was seen that the students of the experimental group who were provided MS with the pedagogic agent were found to have a statistically significant higher level of self-regulation skills than the control group students who were not provided with MS. Several suggestions have been made for the use of pedagogical agent-assisted MS in the design of FC courses.