Introduction: Financial inaccessibility to health services is aggravated in some health zones by armed conflicts. This study analyzes the direct costs of care for children under 5 years old based on the Integrated Management of Childhood Illness approach (PCIME). It compares the direct costs of care with the solvency of the care bill issued according to the pricing applied in hospitals in three health zones (Ibanda, Walungu and Lemera) in South Kivu, in the Democratic Republic of Congo. This province has been experiencing recurrent armed conflicts for thirty years. Methodology: The study is comparative cross-sectional, conducted from January to December 2018 in hospitals and health centers in the health zones of Ibanda, Walungu and Lemera in South Kivu. Data collection mainly relied on documentary review (patient files, hospital registers, laboratory registers, cash books and issued invoices). Data analysis was performed using Excel 2016 and SPPS software. The frequencies, the proportions and the median were identified. The comparison of the proportions was carried out. A logistic regression model testing the associations was applied and one-way analyzes of variance or Pearson’s correlation test were performed for the observed variations. Results: The direct cost of health care for children under 5 years old remains high, although the cost of care for the majority of pathologies is less than or equal to $US50 (p<0.001). The cost of hospitalization per episode of care (≤ $US78) represents the highest cost in the Ibanda Health Zone (ZS) for a non-flat rate. The cost of drugs remains higher (≤ $US20) in the HZ of Lemera, which is more unstable for a flat rate (p<0.001). Households pay 82% of bills. The insolvency of healthcare bills is predominant (89.9% in the rural Health Zone of Lemera with a flat rate (p<0.001)). Certain socio-demographic factors (age of the patients, level of education and socio-professional situation of the parents) explain 48% of the directly proportional increase in the cost of care (p<0.001); while the evolution of the cost is inversely proportional from the rather stable urban Health Zone of Ibanda with non-flat rate to the rural Health Zones of Walungu and Lemera respectively stable and unstable all applying a flat rate (p=0.018). Discussion and Conclusion: Crisis situations have a negative impact on health care costs for children in South Kivu, especially those who are vulnerable. There are, however, differences in the cost of care observed according to the Health Zones in crisis. We recommend a further study including several health zones and dealing with quantitative and qualitative aspects in order to analyze and adapt primary health care financing strategies.