We assessed the reproducibility and validity of a food frequency questionnaire (FFQ) among middle-aged and older adults in Semarang, Indonesia. A total of 259 subjects aged 40–80 years completed two FFQs (nine-month apart) and nine 24 h dietary recalls (24HDRs, as a reference method). The reproducibility of the FFQ was analyzed using correlation coefficient, intra-class correlation coefficient (ICC), weighted kappa statistics and misclassification analysis. The validity was estimated by comparing the data acquired from FFQ1 and 24HDRs. The crude Pearson’s correlation coefficients and ICC for total energy and nutrients between FFQ1 and FFQ2 ranged from 0.50 to 0.81 and 0.44 to 0.78, respectively. Energy adjustment decreased the correlation coefficients for most nutrients. The crude, energy-adjusted and de-attenuated correlation coefficients for FFQ1 and 24HDRs ranged from 0.41 to 0.70, 0.31 to 0.89 and 0.54 to 0.82, respectively. The agreement rates for the same or adjacent quartile classifications were 81.1–94.6% for two FFQs and 80.7–89.6% for FFQ1 and 24HDRs. The weighted kappa values were 0.21 to 0.42 for two FFQs and 0.20 to 0.34 for FFQ1 and 24HDRs. A positive mean difference was found in the Bland–Altman analyses for energy and macronutrients. The FFQ could be acceptable for nutritional epidemiology study among Indonesians.