This systematic review and meta-analysis of randomized controlled trials (RCTs) compared body compositional changes, including fat mass (FM), body fat percentage (BF%), and fat-free mass (FFM), between different types of high-intensity interval training (HIIT) (cycling vs. overground running vs. treadmill running) as well as to a control (i.e., no exercise) condition. Meta-analyses were carried out using a random-effects model. The I² index was used to assess the heterogeneity of RCTs. Thirty-six RCTs lasting between 3 to 15 weeks were included in the current systematic review and meta-analysis. RCTs that examined the effect of HIIT type on FM, BF%, and FFM were sourced from online databases including PubMed, Scopus, Web of Science, and Google Scholar up to 21 June 2022. HIIT (all modalities combined) induced a significant reduction in FM (weighted mean difference [WMD]: −1.86 kg, 95% CI: −2.55 to −1.18, p = 0.001) despite a medium between-study heterogeneity (I² = 63.3, p = 0.001). Subgroup analyses revealed cycling and overground running reduced FM (WMD: −1.72 kg, 95% CI: −2.41 to −1.30, p = 0.001 and WMD: −4.25 kg, 95% CI: −5.90 to −2.61, p = 0.001, respectively); however, there was no change with treadmill running (WMD: −1.10 kg, 95% CI: −2.82 to 0.62, p = 0.210). There was a significant reduction in BF% with HIIT (all modalities combined) compared to control (WMD: −1.53%, 95% CI: −2.13, −0.92, p = 0.001). All forms of HIIT also decreased BF%; however, overground running induced the largest overall effect (WMD: −2.80%, 95% CI: −3.89 to −1.71, p = 0.001). All types of HIIT combined also induced an overall significant improvement in FFM (WMD: 0.51 kg, 95% CI: 0.06 to 0.95, p = 0.025); however, only cycling interventions resulted in a significant increase in FFM compared to other exercise modalities (WMD: 0.63 kg, 95% CI: 0.17 to 1.09, p = 0.007). Additional subgroup analyses suggest that training for more than 8 weeks, at least 3 sessions per week, with work intervals less than 60 s duration and separated by ≤90 s active recovery are more effective for eliciting favorable body composition changes. Results from this meta-analysis demonstrate favorable body composition outcomes following HIIT (all modalities combined) with overall reductions in BF% and FM and improved FFM observed. Overall, cycling-based HIIT may confer the greatest effects on body composition due to its ability to reduce BF% and FM while increasing FFM.