Background This study aimed to investigate the relationship between household wealth and under-5 year mortality in rural and semi-urban Burkina Faso. Methods The study included 15 543 children born between 2005 and 2010 in the Nouna Health and Demographic Surveillance System. Information on household wealth was collected in 2009. Two separate wealth indicators were calculated by principal components analysis for the rural and the semi-urban households, which were then divided into quintiles accordingly. Multivariable Cox proportional hazards regression was used to study the effect of the respective wealth measure on under-5 mortality. Results We observed 1201 childhood deaths, corresponding to 5-year survival probability of 93.6% and 88% in the semi-urban and rural area, respectively. In the semi-urban area, household wealth was significantly related to under-5 mortality after adjustment for confounding. There was a similar but non-significant effect of household wealth on infant mortality, too. There was no effect of household wealth on under-5 mortality in rural children. Conclusions Results from this study indicate that the more privileged children from the semi-urban area with access to piped water and electricity have an advantage in under-5 survival, while under-5 mortality in the rural area is rather homogeneous and still relatively hig