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• We examined the impact of COVID-19-related behavioral restrictions in Japan. • Scant studies focused on university students' mental health during the pandemic. • COVID-19 negatively impacted upper-level university students' mental health. • Fourth-year students had greater mental health changes than did their counterparts. • This research informs public health interventions and programs. This study aimed to investigate the differences in mental health during COVID-19, specifically among second-, third-, and fourth-year Japanese university students (n = 2,157; n = 2,000; and n = 2,284; respectively). A one-way MANOVA was conducted to assess the association between year of enrollment (academic years 2020, 2021, and 2022) and each of the eight subscales of the counseling Center Assessment Psychological Symptoms-Japanese. For second-year students, depression and generalized anxiety mean scores were higher in 2021 than those in 2020 and 2022. Alcohol use mean scores got smaller each year. For third-year students, depression, generalized anxiety, social anxiety, hostility, and alcohol use were significantly higher in 2021 than those in 2020 and 2022. Among fourth-year students, means for all eight subscale categories were significantly higher in 2021 than those in 2020 and 2022. The findings found worsened mental health profiles during 2021, which recovered to approximate pre-pandemic levels in 2022. This study demonstrates that university students' mental health has been negatively impacted by the COVID-19 pandemic, an effect which is more salient among fourth-year students. Further, it offers insights into mental health trends among Japanese university students and a possible foundation for learning about changes among university students worldwide. [ABSTRACT FROM AUTHOR]