Background: Microvascular changes and precursors of atherosclerosis are frequently observed in young patients with early-onset type 1 diabetes (T1DM). Due to their known beneficial effects, physical activity is strongly recommended for its management. Objectives: This study aimed to investigate the effects of eight weeks of organized exercise (OE) and non-organized leisure time activity (NOLTA) on determinants of cardiovascular disease and physical fitness in children with type 1 diabetes. Methods: In this quasi-experimental study, 20 children with T1DM were randomly divided into two groups of 10: OE (n = 10, mean age = 12.60 ± 1.34 years) and NOLTA (n = 10, mean age = 12.40 ± 0.84 years). Subjects in both groups participated in their respective activities 3 days per week. Blood samples and physiological measurements were taken 48 hours before and after the 8-week training period. Results: High-density lipoprotein (HDL) levels and physical fitness factors increased significantly in both exercise groups. Fasting blood glucose, C-reactive protein, and the cholesterol/HDL ratio were also significantly reduced in both groups. Waist circumference, glycosylated hemoglobin, and the LDL/HDL ratio were significantly reduced only in the OE group. However, the decrease in the acute phase protein pentraxin 3 was minimal and statistically insignificant. Conclusions: In children and adolescents with T1DM, regular exercise—due to its anti-inflammatory effects and its ability to improve cardiorespiratory fitness, lipid profile, and blood glucose levels—may help reduce the severity and likelihood of cardiovascular disease in adulthood.