Background: This study analysed through the perspective of networks the association between physical activity (PA), sedentary behaviour (SB), and cardiovascular risk factors in overweight low-income schoolchildren from the perspective of complex systems. Methods: The sample consisted of 41 overweight children between 6 and 10 years old (56% girls). PA and SB were analysed by accelerometer, and the measures of cardiovascular factor risk were: anthropometric and hemodynamic measurements, body fat, lipid profile and glucose, cardiorespiratory fitness (CRF), left ventricular mass (LVM), and Sokolow–Lyon. Network analysis with Bootstrap-1000 was performed to analyse the association between PA, SB and the cardiovascular risk factors. Results: Moderate-to-vigorous PA was positive related to waist circumference (WC; 0.499), HDL-C (0.307), and CRF (0.276), and negatively associated with BMI (−0.251) and Fat (−0.341). For SB, positive associations were seen with WC (0.326), CRF (0.296), LVM (0.250) and Sokolow (0.215). In addition, the centrality indicators highlighted WC as the most important variable in the network. Conclusion: Interventions that aim to mitigate the harmful effects of obesity on cardiovascular risk factors in overweight children should consider WC as an important variable in the system.