This longitudinal study examines the impact of involuntary and prolonged online education on the mental health (anxiety and stress) of university students during the COVID-19 pandemic. An electronic questionnaire was administered to 6,242 students enrolled in public affairs courses in four Jordanian universities. When compared with the pre-COVID-19 situation, the students reported experiencing higher levels of anxiety and stress and suffered persistently. Multiple regression analyses showed that anxiety and stress were influenced by several personal and non-personal factors. ANOVA analysis revealed that after 1 year of online education, students were worried about the quality of in-class learning, adequate training, and the political skills that they could gain, including their ability to build a rapport with instructors. Continuing to impose online education as the only way to deliver classes has had negative impacts on students' mental health. Thus, new ways of designing and delivering public affairs courses are needed.