BACKGROUND: Safe disposal of children's faeces has always been one of the main challenges to good hygiene in Ghana. Although it has been proven that children's faeces are more likely to spread diseases than adults' faeces, people usually mistake them for harmlessness. This study, therefore, sought to determine the prevalence and factors associated with safe disposal of children's faeces in Ghana. METHODS: Data from the 2014 Ghana Demographic and Health Survey was used for the analysis. A sample size of 2228 mother-child pairs were used for the study. The outcome variable was disposal of children stools. Both bivariate and multivariable logistic regression analyses were performed to identify the factors with safe child stool disposal. RESULTS: The prevalence of safe child stool disposal in Ghana was 24.5%. Women in the middle [Adjusted odds ratio (AOR) = 4.62; Confidence Interval (CI) = 3.00-7.10], Coastal Zone [AOR = 4.52; CI = 2.82-7.22], mothers whose children were aged 12-17 [AOR = 1.56; CI = 1.15-2.13] and 18-23 months [AOR = 1.75; CI = 1.29-2.39], and mothers whose household had improved type of toilet facility [AOR = 2.04; CI = 1.53-2.73] had higher odds of practicing safe children's faeces disposal. However, women from households with access to improved source of drinking water [AOR = 0.62; CI = 0.45-2.7] had lower odds of practicing safe children's faeces disposal. CONCLUSION: Approximately only about 25 out of 100 women practice safe disposal of their children's faeces in Ghana. The age of the child, ecological zone, the type of toilet facilities, and the type of drinking water source are associated with the disposal of child faeces. These findings have proven that only improved sanitation (i.e. drinking water and toilet facilities) are not enough for women to safely dispose of their children's faeces. Therefore, in addition to provision of toilet facilities especially in the northern zone of Ghana, there is also the need to motivate and educate mothers on safe disposal of children's stools especially those with children below 12 months. More so, mothers without access to improved toilet facility should also be educated on the appropriate ways to bury their children's stools safely.