Background- Annually 1 million newborns worldwide die of infection caused by bacteria that enter the body via the umbilical cord. Regarding this the Ethiopia national strategy of new born and child survival identified Chlorhexidine as one of the high impact interventions to minimize neonatal mortality. Whereas, studies have shown Human breast milk application to the neonatal umbilical cord has a shorter cord separation time and lower rate of infection than Chlorhexidine or dry cord care. Method- From May to November, 2018, a three arm, non- masked, community based, cluster randomized controlled trial was conducted at Butajira Demographic and Health Surveillance site located in the Gurage Zone of the Southern Nations, Nationalities and Peoples´ Region of Ethiopia. Nine sub districts of the Butajira Demographic and Health Surveillance site were randomized into two intervention groups that are human breast milk and Chlorhexidine and a control group which is the dry cord care using a lottery method. From a sample size of 337, data were entered and analyzed for 302 term singleton newborns. Baseline characteristics across the groups were compared by ANOVA for continuous variables and Chi square for categorical variables. Mean cord separation time was compared among the groups using one way ANOVA whereas the secondary outcome i.e. rate of omphalitis was expressed in terms of frequency and was compared among the groups using Chi square. Level of significance was set at p <0.05 with 95% confidence interval. Result- The mean cord separation time was 5.6 days in the human breast milk group, 5.9days in the Chlorhexidine group, and 5.7days in the dry cord care group but this difference was not statistically significant among the study groups (p value=0.40). The highest signs of cord infection rate were observed in the dry care group and this was significant regarding the redness on the base of the cord stump (P<0.001). Conclusion- Topical application of human breast milk is related with shorter cord separation time compared to chlorhexidine or dry cord care. It also has reduced incidence of infection, as much as topical chlorhexidine application. Generally the readily available human breast milk should be given further emphasis.Trial registration- This trial is registered at the Pan African Clinical Trial Registry on 27th August 2020 with a clinical trial registration number of PACTR202008804462886 . It can be accessed using the URL address:https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=593.