This study aimed to investigate cardiovascular and cardiorespiratory adaptations to exercise intervention among participants who showed higher (responders–RsBFP) and lower (non-responders–NRsBFP) levels of body fat percentage (BFP) responsiveness. Adolescents (42.5% males) participated in a ten-week school-based high-intensity interval training (HIIT), followed by a comparison of BFP, blood pressure (BP), and cardiorespiratory fitness (CRF). RsBFP age of 16.15 ± 0.36 years, body height 170.82 ± 8.16 cm, weight 61.23 ± 12.80 kg, and BMI 20.86 ± 3.29 kg/m2. Meanwhile, NRsBFP age of 16.04 ± 0.36 years, body height 168.17 ± 8.64 cm, weight 57.94 ± 8.62 kg, and BMI 20.47 ± 2.24 kg/m2. HIIT intervention impacted BFP, with a higher decrease in the RsBFP than the NRsBFP (ΔBFPRs = − 2.30 ± 3.51(10.34%) vs. ΔBFPNRs = 1.51 ± 1.54(6.96%) p < 0.001). The primary comparison showed a statistically significant interaction effect in relation to CRF (F(1,71) = 14.12; p < 0.001). Detailed comparisons showed large and significant CRF changes in RsBFP (7.52%; d = 0.86; p < 0.001) but not in NRsBFP (2.01%; d = 0.11; p = 0.576). In addition, RsBFP and NRsBFP benefited equally in SBP (5.49%, d = 0.75; p < 0.001; 4.95%, d = 0.74; p < 0.001, respectively). These findings highlight that exercise benefits on body fat may be mainly related to gains in CRF. Due to substantial intra-individual variability in adaptation, there is a need for personalized intervention tailored for those with different reaction thresholds in body mass components.