The aims were to investigate the changes in physical activity of university students after the COVID-19 emergency declaration was lifted, and to determine whether there were any differences in these changes between academic years. The subjects were 81 students attending university or graduate school in Kochi Prefecture who completed a baseline survey (May 2020). Analysis 1, included 51 subjects who responded to both the baseline survey and the retrospective survey (October 2020) on physical activity at 1 year prior. In Analysis 2, 71 subjects who participated in at least one follow-up examination (August 2020, November 2020) were included. The International Physical Activity Questionnaire – Long Form was used to assess physical activity and sitting time per week. Between October 2019 and May 2020, the total (-47.7%), vigorous (-59.3%) and moderate (-42.1%) physical activity decreased, and sitting time (+36.9%) increased. The interaction between the time of the survey and year of university (first-year, ≥second-year), analyzed using a generalized linear mixed model, on total, vigorous, walking physical activity and sitting time was significant. Especially, the estimate of least squares mean after inverse square root transformation of total physical activity in first-year students was higher in November 2020 (8192.4 METs·min/week) compared to baseline (3388.5 METs·min/week). Vigorous physical activity in first-year students was also higher in November 2020 (4773.3 METs·min/week) compared to baseline (1060.3 METs·min/week). The emergency declaration in April 2020 inhibited physical activity among university students, and the impact was particularly strong among first-year students.