This study aimed to compare the effects of a combined high-intensity interval training (HIIT) and small-sided games (SSG) training program (SSG + HIIT) with training programs consisting solely of either HIIT or SSG on the cardiometabolic and physical fitness of sedentary, overweight youth. A randomized, parallel-controlled study design was employed, with interventions lasting six weeks (twice a week, with each work time lasting 12-16 minutes). Fifty-seven sedentary, overweight male youth participants (15.1 ± 0.8 years) were assessed twice on anthropometric measures, blood pressure, endurance (using the Multi-Stage Fitness Test, MSFT), muscle power (countermovement jump and broad jump), and change of direction ability (using the 5-0-5 COD test). The session's ratings of perceived exertion (RPE) and scores on the Physical Activity Enjoyment Scale (PACES) were also monitored. The HIIT group exhibited a significantly smaller waist circumference compared to the control group (p = 0.041) after the intervention. The control group exhibited a significantly worst COD deficit compared to the SSG + HIIT (p = 0.002), SSG (p = 0.001) and HIIT (p = 0.048) after the intervention. In the case of MSFT, the group exhibited a significantly smaller distance covered than SSG + HIIT (p = 0.002), and SSG (p = 0.005). Moreover, significant differences on RPE (p < 0.001) and PACES (p < 0.001) was found between groups. The SSG + HIIT or SSG are effective for improving COD and aerobic capacity, while being more enjoyable and less intense than HIIT alone. However, HIIT is more effective in reducing waist circumference. The research limitations include the short intervention duration, lack of control for diet and external factors, and the need for longer-term research.