NOVA is a food classification system that categorises food items into one of four categories according to the extent and purpose of their processing: minimally processed food (MPF), processed culinary ingredient (PCI), processed food (PF), or ultra-processed food (UPF). The aim of this study was to determine the relative validity and reproducibility of a food frequency questionnaire (EAT5 FFQ) for measuring daily energy intake (EI kJ) and percentage of daily energy intake (EI%) from each NOVA group in New Zealand children. One hundred parents of five year old children completed the 123 item EAT5 FFQ on two occasions four weeks apart. A 3 day weighed diet record (WDR) was completed on non-consecutive randomly assigned days between FFQ appointments. The FFQ overestimated EI (both as kJ and %) from MPF and UPF, and underestimated intakes from PCI and PF, compared with the WDR. Bland–Altman plots indicated reasonably consistent agreement between FFQ and WDR for MPF and UPF but not PCI or PF. Correlation coefficients between the FFQ and WDR were acceptable for EI (%) for MPF (r = 0.31) and UPF (r = 0.30). The FFQ differentiated between the highest and lowest quartiles for EI (%) from MPF and UPF foods (p-values for the trends were 0.006 and 0.009 respectively), and for EI (kJ) from UPF foods (p-value for trend 0.003). Bland–Altman plots indicated consistent agreement between repeat administrations of FFQ for MPF and UPF only, while intra-class correlations suggested good reproducibility for EI (kJ and %) for all four NOVA categories (range 0.51–0.76). The EAT5 FFQ has acceptable relative validity for ranking EI (%) from MPF and UPF. It has good reproducibility for measuring EI from all four NOVA categories, in young children.