Background: Salmonella and Shigella is a major health problem worldwide, in developing countries like Ethiopia, it is responsible for high morbidity and mortality of children. This study aimed to determine the prevalence of Salmonella and Shigella infection, their antibiotic susceptibility pattern and associated risk factor among the diarrheic pediatrics patients that visited Alamura Health Center in southern Ethiopia. Method: A facility based cross-sectional study was conducted at Alamura Health Center from April 2018 – July 2019. The study was performed on pediatrics below the age of 14 years in which consecutive children with diarrhea were included for the study. A structured questionnaire was used to collect socio-demographic and clinical data after assent and consent obtained from parents or care taker. The stool sample cultured as per the standard operating procedure (SOP) of the microbiology laboratory. Antibiogram was performed by Kirby-Bauer disc diffusion method and was interpreted based on the Clinical and laboratory standard institute guidline (CLSI) version 2018. Results: Out of 263 children enrolled in the study, 50.5 % were females. The overall, 21/263 (8 %) 95% CI, (4.6 - 11.4%) Shigella and Salmonella was isolated. Shigella dysenteriae was dominantly isolated 11 (4.2%) followed by 9(3.42%) Shigella spp, and 1(0.38%) Salmonella typhi. Those with habit of washing the hands of children after toilet sometimes (AOR = 235.1, 95% CI, 20.9 - 2643.3, P = .000) and store cooked food in open container for later use (AOR = 36.44, 95% CI, 5.82 - 228.06, P = .000) showed statistically significant association. Conclusion: High level of Shigella spp and one Salmonella was isolated from diarrheic children at Alamura Health Center. Shigella dysentery was the most dominantly isolated. Those practised hands wash for their child after defecation for sometimes was 235.1-fold at risk of infection. Similarly, those store foods for later use in an open container was 36.44 times at risk of infection. Therefore, to alleviate this infection the concerned body should focus on giving health education for hand wash after defecation and storing food in a closed container later use is mandatory.