Introduction Poor health seeking behaviour continues to be major challenge in accessing healthcare in sub-Saharan Africa despite the availability of effective treatment for most childhood illnesses. The current study investigated the barriers to healthcare access and health seeking for childhood illnesses in Burundi. Methods The study utilized data from the 2016-17 Burundi Demographic and Health Survey (BDHS). A total of 2173 children under five of childbearing women were included in our study. The outcome variable for the study was healthcare seeking for childhood illnesses (diarrhea and fever/cough). Barriers to healthcare access were the explanatory variables and maternal and child factors were the control variables. Chi-square test of independence and a binary logistic regression modelling were carried out to generate the results. Results Overall, less than 50% of children in Burundi who were ill two weeks before the survey obtained healthcare. We found that children of mothers who perceived getting money for medical care for self as a big problem [aOR = 0.75; CI = 0.60-0.93] and considered going for medical care alone as a big problem [aOR = 0.71; CI = 0.55-0.91] had lower odds of getting healthcare, compared to those of mothers who considered these indicators as not a big problem. The results also showed that children of mothers who had three [aOR = 1.48; 1.02-2.15] and four [aOR = 1.62; 1.10-2.39], children were more likely to get healthcare for childhood illnesses compared to those whose mothers had one child. Children of mothers with single birth children were less likely to get healthcare compared to those whose mothers had multiple births. Conclusion Findings of the low prevalence of healthcare for childhood illnesses in Burundi suggest the need for government and non-governmental health organizations to strengthen women's healthcare accessibility for child healthcare services and health seeking behaviours. The Burundian government through multi-sectoral partnership should strengthen health systems for maternal health and address structural determinants of women's health by creating favourable conditions to improve the status of women and foster their overall socioeconomic well-being. Free child healthcare policies in Burundi should be strengthened to enhance the utilization of child healthcare services in Burundi.