Preventive chemotherapy (PC), the main strategy recommended by the World Health Organization to eliminate soil-transmitted helminthiasis (STH) and schistosomiasis (SCH), should be strengthened through identification of the remaining SCH transmission foci and evaluating its impact to get a lesson. This study was aimed to assess the prevalence of STH/SCH infections, the intensity of infections, and factors associated with STH infection among school-aged children (SAC) in Uba Debretsehay and Dara Mallo districts (previously not known to be endemic for SCH) in southern Ethiopia, October to December 2019. Structured interview questionnaire was used to collect household data, anthropometric measurements were taken and stool samples collected from 2079 children were diagnosed using the Kato-Katz technique. Generalize mixed-effects logistic regression models were used to assess the association of STH infections with potential predictors. A P-value less than 0.05 was considered statistically significant. The prevalence of Schistosoma mansoni in the Dara Mallo district was 34.3% (95%CI 30.9–37.9%). Light, moderate, and heavy S. mansoni infections were 15.2%, 10.9%, and 8.2% respectively. The overall prevalence of any STH infection was 33.2% with a 95% confidence interval (CI) of 31.1–35.3%. The intensity of infections was light (20.9%, 11.3% & 5.3%), moderate (1.1%, 0.1% & 0.4%) and heavy (0.3%, 0% & 0%) for hookworm, whipworm and roundworms respectively. The overall moderate-to-heavy intensity of infection among the total diagnosed children was 2% (41/2079). 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 housewife (AOR = 0.5; 95%CI 0.3–0.8), middle [AOR = 1.1; 95%CI 1.0–1.3] or high [AOR = 0.7; 95%CI 0.5–0.9] socioeconomic status. Dara Mallo district was moderate endemic for S. mansoni; and it needs sub-district level mapping and initiating a deworming campaign. Both districts remained moderate endemic for STH. Evidence-based strategies supplementing existing interventions with the main focus of the identified factors is important to realize the set targets.