Increasing prevalence of sedentary behavior (SB) combined with low levels of physical activity (PA) in children and adolescents has become a growing public health concern. Therefore, this study aimed to identify the daily behavioral pattern of adolescents and examine the isotemporal substitution effects of SB with light-intensity PA (LIPA) or moderate-to-vigorous PA (MVPA) on cardiometabolic markers. In this cross-sectional study, the daily behavioral pattern of Brazilian male adolescents was objectively measured for 7 days. Vector magnitude activity counts were used to estimate SB, LIPA, and MVPA with cut-points specifically validated for youth. The isotemporal substitution model was used to assess the effects of replacing different SB bouts (5, 10, 30, and 60 min) with LIPA or MVPA on cardiometabolic markers [body mass index, waist circumference, body fat percentage (BF%), total cholesterol, high-density lipoprotein cholesterol (HDL-C), non-HDL-C, low-density lipoprotein cholesterol, triglyceride (TG), glucose, insulin, homeostatic model assessment of insulin resistance (HOMA2-IR), insulin sensitivity (HOMA2-S), beta cell function (HOMA2-β), systolic-blood pressure (SBP), diastolic-blood pressure, and cardiometabolic risk score]. Male adolescents (n = 84; age, 16.7 ± 0.9 years) wore the GT3X+ for 6.7 ± 0.6 days, during 15.2 ± 2.3 h, and spent 72.9% of the time in SB, 17.3% in LIPA, and 9.8% in MVPA. SB replacement with LIPA was associated with increased HDL-C, TG, HOMA2-IR, and HOMA2-S and decreased SBP. In contrast, SB replacement with MVPA was associated with decreased BF%. Therefore, our findings suggest that replacing SB with LIPA showed positive results on HDL-C, HOMA2-S and SBP, while replacing SB with MVPA was associated with only one obesity indicator (BF%). Moreover, participants met the daily MVPA recommendations, but they still had a daily behavioral pattern with high SB. In this context, LIPAs can be considered an effective alternative to reduce SB and improve the health indicators of this population.