Objectives To compare the effects of interval training and moderate-intensity continuous training (MOD) on body adiposity in humans, and to perform subgroup analyses that consider the type and duration of interval training in different groups. Design Systematic review and meta-analysis. Data sources English-language, Spanish-language and Portuguese-language searches of the electronic databases PubMed and Scopus were conducted from inception to 11 December 2017. Eligibility criteria for selecting studies Studies that met the following criteria were included: (1) original articles, (2) human trials, (3) minimum exercise training duration of 4 weeks, and (4) directly or indirectly compared interval training with MOD as the primary or secondary aim. Results Of the 786 studies found, 41 and 36 were included in the qualitative analysis and meta-analysis, respectively. Within-group analyses showed significant reductions in total body fat percentage (%) (interval training: −1.50 [95% CI −2.14 to −0.86, p<0.00001] and MOD: −1.44 [95% CI −2.00 to −0.89, p<0.00001]) and in total absolute fat mass (kg) (interval training: −1.58 [95% CI −2.74 to −0.43, p=0.007] and MOD: −1.13 [95% CI −2.18 to −0.08, p=0.04]), with no significant differences between interval training and MOD for total body fat percentage reduction (−0.23 [95% CI −1.43 to 0.97], p=0.705). However, there was a significant difference between the groups in total absolute fat mass (kg) reduction (−2.28 [95% CI −4.00 to −0.56], p=0.0094). Subgroup analyses comparing sprint interval training (SIT) with MOD protocols favour SIT for loss of total absolute fat mass (kg) (−3.22 [95% CI −5.71 to −0.73], p=0.01). Supervised training, walking/running/jogging, age (<30 years), study quality and intervention duration (<12 weeks) favourably influence the decreases in total absolute fat mass (kg) observed from interval training programmes; however, no significant effect was found on total body fat percentage (%). No effect of sex or body mass index was observed on total absolute fat mass (kg) or total body fat percentage (%). Conclusion Interval training and MOD both reduce body fat percentage (%). Interval training provided 28.5% greater reductions in total absolute fat mass (kg) than MOD. Trial registration number CRD42018089427.