Background In developing countries particularly in sub-Saharan Africa trachoma is still a public health concern. Ethiopia is the most affected of all and bears the highest burden of active trachoma. In spite of this, the prevalence of active trachoma among the pastoralist population in Ethiopia not yet disclosed. The aim of this study was to determine the prevalence of active trachoma and associated risk factors among children in a pastoralist population in Madda Walabu rural district, Ethiopia. Methods A community-based cross-sectional study was conducted among children in a pastoralist population in Madda Walabu rural district, from May 1 to 30, 2017. A systematic sampling technique was employed to select 409 children’s. Simplified WHO classification scheme was used to assess trachoma. Descriptive and logistic regression analyses were performed. Results A total of 406 children aged 1–9 years have participated, 89 (22%) [95%CI: 18.0–25.6%] were positive for active trachoma. Of these cases, 75(84%) had TI alone in one or both eyes, 14(16%) had TF alone in one or both eyes, and none of the children had both TI and TF. The odds of having active trachoma among children from households using river/ponds, unprotected well/spring and rainwater as their source of drinking water were higher than those from households using water from piped or public tap water (AOR:13,95%CI: 2.9, 58.2), (AOR: 6.1, 95%CI:1.0,36.5) and (AOR: 4.8, 95%CI:1.3,17.8) respectively. Children’s from households that lacked a latrine (AOR: 2.5, 95% CI: 1.8, 5.3), children who did not wash their face by using soap (AOR: 4.3, 95% CI: 1.8, 10.6) and children from households within 16–30 min of water source (AOR: 8.7, 95% CI: 2.20, 34.2) were higher odds of having active trachoma. Conclusions The findings of this study revealed that close to one-quarter of the total children screened for trachoma were positive for the disease. The finding implies that trachoma is still a major concern among children of the pastoralist community which demands further attention of the district health office. Again, intervention with the A, F and E components of SAFE strategy is strongly recommended. Electronic supplementary material The online version of this article (10.1186/s12879-019-3992-5) contains supplementary material, which is available to authorized users.