Background: Preventive chemotherapy (PC), is the main elimination strategy against Soil-Tansmitted Helmenthiasis (STH) and Schistosomiasis (SCH) recommended by the world health organization (WHO), should be strengthened through identification of the remaining SCH transmission foci and evaluating its impact to get lesson. This study was aimed to assess the prevalence of STH/SCH infections, intensity of infections and associated factors among School Age Children (SAC) in two districts, previously not known to be endemic for SCH in Southern Ethiopia, October to December 2019.Methods: Structured interview questionnaire was used to collect data, the record of treatment coverage against STH was reviewed and stool samples collected from 2114 children were diagnosed using Kato-Katz technique. Multilevel logistic regressions were used to assess the association of infections with potential predictors. Results: The reviewed treatment coverage ranges from 92% to 106% in both districts. The prevalence of STH infection was 33.3% with 95% confidence interval (CI) of 31.3% to 35.4%. The intensity of infections was light (93.8%, 99.2% & 92.5%), moderate (4.7%, 0.8% & 7.5%) and heavy (1.5%, 0% & 0%) for hookworm, whipworm and Roundworms respectively. STH infection was higher among male SAC with Adjusted Odds Ratio (AOR) of 1.7; 95%CI: 1.4-2.1); occupation of the household head other than farmer or house wife (AOR=0.6; 95%CI: 0.4-0.9) and with higher wealth index (AOR=0.7; 95%CI: 0.5-0.9) as compared to the poorest one. The prevalence of S.mansoni in Dara Mallo district was 34.5% (95%CI: 31.1-38.1%). Light, moderate and heavy S.mansoni infections were 42.9%, 33.7% and 23.4% respectively. Children from mothers aged 50 or above years were significantly more likely infected by S.mansoni (AOR=5.9; 95%CI: 1.4-27.4) as compared to children from mothers (caretakers) of 34 or lower age.Conclusions: Though high PC coverage were reported, STH remained moderately endemic while S.mansoni became moderate endemic in Dara Mallo, requiring sub-district level mapping and deworming campaign initiations. Evidence based strategies which supplement the existing interventions focusing on the identified factors are important to realize the set targets.