Universal healthcare has been proposed as a strategy to achieve health equity. Herein, we describe childhood cancer survival disparities within a universal healthcare system in Cali, the third largest city in Colombia. We prospectively included data from Cali's childhood cancer surveillance system (VIGICANCER) cohort (2009–2016) and adjusted the hazard ratios (aHR) for confounders using multivariate Cox regression. We included 1808 patients with a median age for children (n = 1499) of 6 years and for adolescents (n = 309) of 17 years. Fifty-six percent were male, 14% were afro-descendants, 61% resided outside of Cali, 52% had public insurance, 44% had private insurance, and 4% were uninsured. Five-year overall survival rates for patients with private insurance, public insurance and uninsured patients were 62% (95% CI: 58, 66), 43% (95% CI: 39, 46) and 23% (95% CI: 13, 35), respectively. Compared to private insurance, mortality among patients with public insurance (aHR = 1.6; 95% CI: 1.3, 1.9) and uninsured (aHR = 2.7; 95% CI: 1.9, 4.0) was higher. We found significant disparate survival outcomes, primarily by insurance and tumor type. Higher treatment abandonment, higher treatment-related mortality, and advanced disease at diagnosis partially explained these disparities. Survival inequalities persist in Colombia despite an established universal healthcare system aimed at providing equal care for all.