OBJECTIVES To investigate the impact of complex chronic conditions on the use of healthcare resources and hospitalization costs in a pediatric ward of a public tertiary referral university hospital in Brazil. METHODS This is a longitudinal study with retrospective data collection. Overall, three one-year periods, separated by five-year intervals (2006, 2011, and 2016), were evaluated. Hospital costs were calculated in three systematic samples of 100 patients each, consisting of patients with and without complex chronic conditions in proportion to their participation in the studied year. RESULTS Over the studied period, the hospital received 2,372 admissions from 2,172 patients. The proportion of hospitalized patients with complex chronic conditions increased from 13.3% in 2006 to 16.9% in 2016 as a result of a greater proportion of neurologically impaired children, which rose from 6.6% to 11.6% of the total number of patients in the same period. Patients’ complexity also progressively increased, which greatly impacted the use of healthcare resources and costs, increasing by 11.6% from 2006 (R$1,300,879.20) to 2011 (R$1,452,359.71) and 9.4% from 2011 to 2016 (R$1,589,457.95). CONCLUSIONS Hospitalizations of pediatric patients with complex chronic conditions increased from 2006 to 2016 in a Brazilian tertiary referral university hospital, associated with an important impact on hospital costs. Policies to reduce these costs in Brazil are greatly needed.