We examined the reproducibility and relative validity of two measures of overall diet quality, the Healthy Eating Index-2015 (HEI-2015) and Nutrient-Rich Food Index 9.3 (NRF9.3), as estimated by well-established self-administered dietary assessment questionnaires for the Japanese, namely the comprehensive diet history questionnaire (DHQ) and the brief diet history questionnaire (BDHQ). Diet was assessed separately by two DHQs and two BDHQs at a 1-year interval and by 16-day weighed dietary records (DRs) in 121 women and 121 men aged 31–81 years. HEI-2015 and NRF9.3 were calculated from each method. The reproducibility correlation for the two questionnaires (intraclass correlation) ranged from 0.53 (HEI-2015 from BDHQ in men) to 0.77 (NRF9.3 from BDHQ in women). The validity correlation between the first questionnaires and DR (Pearson correlation) ranged from 0.37 (NRF9.3 from BDHQ in men) to 0.61 (NRF9.3 from DHQ and BDHQ in women). Bland–Altman plots showed poor agreement between the DHQ or BDHQ and DR, as well as the presence of weak proportional bias. Overall, these data indicate reasonable reproducibility and ranking ability of the DHQ and BDHQ for assessing the HEI-2015 and NRF9.3 and support their usefulness in future epidemiological research on the overall effects of Japanese diets on various health outcomes.