Introduction: The COVID-19 pandemic has caused an increase in levels of anxiety and distress. However, there has been no research evaluating anxiety levels in students in the health sector in Bolivia, specifically Medicine and Physiotherapy students. Objective: Determine anxiety levels in Medicine and Physiotherapy students at the Christian University of Bolivia during the COVID-19 pandemic. Methods: Non-probabilistic, cross-sectional, analytical study for convenience. A survey was conducted between September 7-29, 2020 to 337 students, of them 270 in the career of Medicine and 67 of Physiotherapy. Results: 48.37 % (n = 163) of the students had mild anxiety, 20.18 % (n = 68) mild to moderate anxiety, 11.87 % (n = 40) moderate to severe anxiety, and 19.58 % (n = 66) very severe anxiety. Medical and physiotherapy students had similar levels of anxiety (p = 0.83). It was determined that nationality (p = 0.80), age (p = 0.83), whether if they live alone or not (p = 0.35), and academic year of study (p = 0.09) are not associated with the level of anxiety of students. It was found that the sex of the students has a relationship with the levels of anxiety: women presented higher levels of severe anxiety than men (p = 0.017). It was identified in this research that less than 6% of students receive psychological therapy, regardless of their anxiety levels. Conclusions: The psychological support of the university to its students should be reinforced and research should continue to determine other risk factors that can help create better policies for the prevention of anxiety disorder at the university and national levels.