Background: Metabolic syndrome (MetS) is rapidly increasing in prevalence with rising childhood obesity and sedentary lifestyles worldwide. The aim of this study was to estimate the prevalence of MetS and its components among Sudanese early adolescents in Khartoum State. Methods: A descriptive cross-sectional study was conducted at primary schools in Khartoum State. A questionnaire was administered to assess the sociodemographic characteristics of the participants. Anthropometric, blood pressure, and biochemical measurements were taken. Results: In total, 921 students, boys and girls aged 10–15 years old, participated in the study. The mean age of the participants was 12.59 ± 1.21 years. The overall prevalence rate of MetS was 2.3% using International Diabetes Federation (IDF) criteria. MetS was significantly more prevalent among boys than girls (3.4% vs. 1.5%). Obese adolescents had higher MetS prevalence than those who were overweight (14.9 vs. 2.8, p < 0.001). Conclusion: Boys had a significantly higher prevalence of metabolic syndrome than girls. Early adolescents from Sudan who are obese had more risk factors for MetS than those who are normal weight or overweight. It is important to address the causes of increased risk for MetS early in life to prevent the development of the disease in adult life.