The growing prevalence of overweight/obesity in adolescents highlights the significance of studying metabolic syndrome (MetS) in increasingly sedentary adolescents. To date, no study in Sudan has examined the association between MetS and physical activity (PA) among adolescents. This study aimed to assess the association between MetS and its components and PA among Sudanese early adolescents. A cross-sectional assessment was conducted from to 2018 to 2019 on a sample of 921 primary school students from Khartoum State, Republic of Sudan. MetS was defined according to the International Diabetes Federation criteria and a standardized questionnaire was used to assess PA. Metabolic equivalents of task were calculated, and levels of different intensities of PA (tertiles) were identified accordingly. The association between PA and MetS and its components was assessed using a logistic regression model. The participants comprised 388 boys and 533 girls with a mean age of 12.59 ± 1.21 years. The prevalence of MetS was significantly higher in subjects in the 1st PA tertile (least active) than in the 2nd and 3rd (most active) tertiles of PA, and this difference was observed in both boys and girls. After adjusting for other study factors, the odds of MetS among adolescents in the 1st PA tertile were 7 times higher than those in the highest PA tertile (adjusted odds ratio = 7.01, 95% confidence interval: 1.48, 32.99). A physically inactive lifestyle was associated with higher odds of MetS and its components, especially waist circumference and triglyceride levels, in Sudanese early adolescents. This study highlights the importance of promoting PA in this age group.