Pediatric patients with chronic conditions frequently have unmet care needs, make extensive use of healthcare services, and often encounter fragmented, non-centered care. This study aimed to analyze the differences in the utilization of primary care (PC) and hospital care (HC) services by these patients according to sex, age, and complexity and to identify associated factors. A cross-sectional study was conducted in a basic health area of Madrid, including patients under 18 years. Among these patients, 15.7% had ≥1 chronic disease, 54.1% were male, the average age was 9.5 years, 3.5% had complexity, and 11.3% had multimorbidity. The mean number of contacts/year with the healthcare system was 9.1, including 8.3 contacts/year with PC (4.9 with pediatricians and 1.9 with nurses) and 0.8 contacts/year with HC (0.8 in external consultations and 0.01 hospitalizations). The factors associated with PC utilization were complexity; female sex; European origin; and diseases like asthma, epilepsy, stroke, recurrent urinary infection, attention deficit hyperactivity disorder, and anxiety, while older age was negatively associated. Thyroid disorders were significantly associated with HC utilization. These findings could help guide the design of optimized pediatric patient-centered care approaches to coordinate care across healthcare services and reduce high healthcare utilization, therefore improving the healthcare outcomes and quality of life for these patients.