Introduction: The aim of this study was to assess the exposure to cardiovascular disease (CVD) risk factors in patients with juvenile idiopathic arthritis (JIA). Intima–media complex thickness (IMT), selected metabolic parameters and health behaviors were assessed in the course of the study. Methods: The study included study group, which consisted of 45 patients with JIA and 37 healthy age- and sex-matched children in the control group. Analyses in both groups included anthropometric parameters, laboratory tests, IMT and a questionnaire on exposure to modifiable CVD risk factors. Results: The study confirmed that CVD risk factors were present in both groups of patients. Significantly more children with JIA had abnormal BMI (p = 0.006) compared to the control group. Children in the study group were more likely to consume fruit regularly (p = 0.021) and less likely to consume fast food (p = 0.011) and sweetened beverages (p = 0.042) than children in the control group. Only 1 patient with JIA met criteria for ideal cardiovascular health. Dietary habits were not associated with IMT values, BMI, presence of joint pain or biochemical parameters in the study group. Conclusions: Patients with JIA are exposed to cardiovascular risk factors equally to their healthy peers. Ideal cardiovascular health should be pursued in the pediatric population with particular attention paid to patients with chronic diseases (i.e., JIA). The application of carotid artery IMT measurement in the assessment of CVD risk requires studies on a larger group of patients.