FFQ are one of the most widely used tools of research into nutritional epidemiology, and many studies have been conducted in several countries using this dietary assessment method. The present study aimed to evaluate the relative validity of FFQ, in comparison with other methods, in assessing dietary intake of children and adolescents, through a systematic review. Four electronic databases (Embase, PubMed, Scopus and Web of Science) found sixty-seven articles, which met the inclusion criteria (healthy children and adolescents from 3 to 18 years of age; journal articles written in English, Spanish and Portuguese between 1988 and March 2019; results showing the comparison between the FFQ with other methods of assessment of dietary intake). The articles were analysed by two independent reviewers. A meta-analysis was conducted using correlation coefficients as estimate effects between the FFQ and the reference standard method. Subgroup analysis and meta-regression were performed to identify the probable source of heterogeneity. In fifty-five of the sixty-seven studies, a single dietary assessment method was used to evaluate the FFQ; nine combined the two methods and three used three reference methods. The most widely used reference method was the 24-h recall, followed by the food record. The overall relative validity of the FFQ to estimate energy, macronutrient, certain micronutrient and certain food item intakes in children and adolescents may be considered weak. The study protocol was registered in PROSPERO under number CRD42016038706.