School closures due to the coronavirus disease 2019 (COVID-19) pandemic have worsened mental health problems for children and adolescents worldwide. We aimed to examine the follow-up effectiveness of a transdiagnostic universal prevention program for anxiety of junior high school students after a nationwide school closure during the COVID-19 outbreak in Japan. A total of 117 junior high school students were included in the analysis. We used the Unified Universal Prevention Program for Diverse Disorders (Up2-D2) program; the Up2-D2 comprises cognitive-behavioral and positive psychological interventions provided over twelve 45-minute sessions. The program was originally implemented between June and July 2020, immediately after pandemic-related school closures had ended in Japan. The program assessments were based on students’ responses to a questionnaire incorporating five scales to measure indicators such as internalizing and externalizing problems. Assessments were carried out before, immediately after, two-month, and six-month after implementing the program. Mixed models for the whole sample showed small anxiety improvement effects immediately post-intervention and two-month, and six-month assessments (g = -0.25, g = -0.44, and g = -0.30, respectively). The anxiety reducing effects were even greater for the higher-anxiety group at the post-, 2-month, and 6-month assessments (g = -1.48; g = -1.59; g = -1.06, respectively). Although there was no control group, these results indicate that the transdiagnostic universal prevention intervention reduce only anxiety, but not other outcomes (depression, anger, and self-efficacy) in junior high students returning to school following school closures related to the COVID-19 pandemic in Japan.