The present study aimed to investigate the association between the duration of anti-coronavirus disease 2019 (COVID-19) public health measures and the quality of life (QOL) and mental health of the Japanese public. The present, nationwide, questionnaire-based, cross-sectional study was conducted in September 2021. The cumulative duration in days of anti-COVID-19 public health measures was calculated for each prefecture in the year prior to the survey, and multilevel linear regression analysis was used to determine the association between the duration of these measures and any impairment of QOL or mental health as assessed by the EuroQol 5-dimensions 5-levels (EQ-5D-5L) and the Kessler scale (K6). The study included 28 118 participants from all 47 prefectures. The median duration of public health measures of all prefectures was 179days. Long-term duration of the measures (181-365days) was not independently associated with low EQ-5D-5L (P=0.128) or high K6 (P=0.179) scores after adjusting for potential confounders (Graphical Abstract). Prolongation of the measures may not be associated with a deterioration in the QOL or mental health of the Japanese public. Nevertheless, it may be necessary to reconsider long-term public health measures given the potential they may have to cause collateral damage, such as socioeconomic one.