In the current context, the development of competencies in university students is essential, which allows them to face environmental problems, especially those associated with their field of academic action, critical thinking being essential, which implies conceptualizing, analyzing and making the right decisions. On the other hand, metacognition leads students to be aware of their potential, having the ability to self-regulate their learning. The article aims to determine the relationship between critical thinking and metacognition in times of pandemic in university students of the first cycle of the Faculty of Medicine of a private university in Lima-Peru, with the participation of a selected group of 135 students. Basic research was applied, with a descriptive-explanatory level and correlational design. The results show that there is a significant relationship between critical thinking and metacognition with an r=, 729, which means a medium positive correlation; Therefore, the university must train teachers in the management of different strategies in order to develop critical thinking and metacognition in students. It is concluded on the importance of critical thinking to promote a quality, reflective and transformative education, which links university theoretical knowledge with the daily activities of individuals.