Background Limited access to healthcare among children in sub-Saharan Africa (SSA) is a major cause of poor infant health indicators. Although many speculate that the private sector expansion has overwhelmingly reinforced health systems’ utilization, little is known as to whether and where children are cared for when they are sick. This study investigated health-seeking behavior (HSB) among children from an urban area of Burkina Faso, with respect to disease severity and the type of provider versus children’s characteristics. Methods A cross-sectional population-based study was conducted in Ouagadougou, Burkina Faso using a two-stage sampling strategy. 1,098 households (2,411 children) data were collected. Generalized estimating equations (GEE) were used to analyze providers’ choice for emergency, severe and non-severe conditions; sex-preference was further assessed with a χ2 test. Results Thirty-six percent of children requiring emergency care sought private providers, as did 38% with severe conditions. Fifty-seven percent with non-severe conditions were self-medicated. A multivariable GEE indicated that University-educated household-heads would bring their children to for-profit (instead of public) providers for emergency (OR = 3.51, 95%CI = 1.90; 6.48), severe (OR = 4.05, 95%CI: 2.24; 7.30), and non-severe (OR = 3.25, 95%CI = 1.25; 8.42) conditions. A similar pattern was observed for insured and formal jobholders. Children’s sex, age and gender was not associated with neither the type of provider preference nor the assessed health condition. Conclusion Private healthcare appeared to be crucial in the provision of care to children. The household head’s socioeconomic status and insurance coverage significantly distinguished the choice of care provider. However, the phenomenon of son-preference was not found. These findings spotlighted children’s HSB in Burkina Faso.