Tools to assess intake among children in Latin America are limited. We developed and assessed the reproducibility and validity of a semi-quantitative food frequency questionnaire (FFQ) administered to children, adolescents, and their caregivers in Lima, Peru. We conducted 24-h diet recalls (DRs) and focus groups to develop a locally-tailored FFQ prototype for children aged 0–14 years. To validate the FFQ, we administered two FFQs and three DRs to children and/or their caregivers (N = 120) over six months. We examined FFQ reproducibility by quartile agreement and Pearson correlation coefficients, and validity by quartile agreement and correlation with DRs. For reproducibility, quartile agreement ranged from 60–77% with correlations highest for vitamins A and C (0.31). Age-adjusted correlations for the mean DR and the second-administered FFQ were highest in the 0–7 age group, in which the majority of caregivers completed the FFQ on behalf of the child (total fat; 0.67) and in the 8–14 age group, in which both the child and caregiver completed the FFQ together (calcium, niacin; 0.54); correlations were <0.10 for most nutrients in the 8–14 age group in which the caregiver completed the FFQ on the child’s behalf. The FFQ was reproducible and the first developed and validated to assess various nutrients in children and adolescents in Peru.