Juvenile obesity is associated with insulin resistance, among other comorbidities. In the pathogenesis of insulin-resistance-related diseases, including obesity and diabetes, Vitamin D deficiency is very common. Therefore, the relationship between insulin resistance, body composition, vitamin D level, and cardiorespiratory fitness in obese children and youth were analyzed based on the Children’s Health InterventionaL Trial III project, Germany. Data on vitamin D levels and homeostatic model assessment (HOMA) indices were available from 147 participants (52.4% female; 90.5% obese; 12.3 ± 2.3 years, BMI: 30.5 ± 5.2 kg/m2, BMI standard deviation score (BMI-SDS): 2.52 ± 0.46). Vitamin D levels correlated negatively with the HOMA index, BMI, BMI-SDS, abdominal circumference, and body fat percentage but positively with relative cardiorespiratory fitness (p < 0.05 in each case). In the backward stepwise linear regression analysis, body fat (in kg; β = 0.403) and vitamin D levels (β = −0.154) explained 21.0% of the variance in the HOMA index. In summary, increased body fat and lower vitamin D levels are associated with increased HOMA indices in overweight and obese children and adolescents. In order to prevent potential negative consequences, including the development of manifest Type 2 diabetes, a healthy lifestyle with a vitamin-D-enriched diet and more time spent outdoors should be promoted.