Background Scabies is a public health problem that affects children and elders predominantly. Its burden is higher in resource-poor settings, and scabies has a significant impact on the long-term health of children. In Ethiopia, there is limited information about scabies in children. Therefore, the purpose of this study was to determine the prevalence of scabies and its associated factors among children aged 5–14 years in Meta Robi District, Ethiopia. Methods A community-based cross-sectional study design using a multistage sampling technique was used to collect data from 457 participants by systematic random sampling. Scabies was diagnosed based on the clinical criteria set by the International Alliance for the Control of Scabies (IACS, 2020). Findings The prevalence of scabies among children aged 5–14 years old was 19.26% (95%CI: 17.20–22.52). In addition, over half (54.6%) of identified cases of scabies were of moderate severity. Factors like families’ low income (aOR = 2.72; 95%CI: 1.32–5.59), being a male child (aOR = 1.96, 95%CI: 1.61–4.01), using only water for hand washing (aOR = 2.01, 95%CI: 1.84–4.79), having a contact history of scabies/skin lesions (aOR = 4.15, 95%CI: 2.02–13.67), and sharing sleeping beds (aOR = 6.33, 95%CI: 2.09–19.13) were significantly associated with scabies. Conclusion The study highlights a high prevalence of scabies among children aged 5–14 years in the district. Provision of adequate health education for the community and children about the scabies and delivering mass drug administration to the district is suggested.