Onchocerciasis transmission in the Ulanga District of Morogoro-Tanzania is still ongoing despite more than 20 years of Community Directed Treatment with Ivermectin (CDTI) in the area. Even though surveys conducted over the years in the area have revealed a decrease in the prevalence of onchocerciasis, the prevalence of comorbidities suggested to be associated with this filarial infection, as epilepsy, is rising in endemic regions. This fact suggests continued transmission ofOnchocerca volvulusand emphasizes the need for the evaluation of factors associated with it among school aged children. Therefore, this study determined the current burden of onchocerciasis in children aged 6 to 12 years and factors associated with continued transmission despite more than 20 years of CDTI in Ulanga District, Morogoro Region-Tanzania. A school-based cross-sectional study was conducted among 270 children aged 6 to 12 years in Ulanga District. Participants were tested using the OV-16 IgG4 Rapid Test. An interview-administered questionnaire was used to assess disease-associated symptoms, knowledge of onchocerciasis, and factors associated with continued transmission of the disease among participants. Descriptive statistics, chi-square test, and logistic regression were performed during data analysis. The prevalence of onchocerciasis was 19.6% (53/270), with boys being more infected; prevalence increased with increasing age groups and was higher in rural areas. Sex (AOR = 2.2, 95% CI: 1.13–4.28), age group of 11–12 years (AOR = 31.45, 95% CI: 2.73–362.27), and not taking ivermectin (AOR = 3.17, 95% CI: 1.53–6.58) were the only significant factors identified to be associated with the transmission of onchocerciasis in this study. The high prevalence of onchocerciasis among school age children in Ulanga district suggests continued transmission in the area. Therefore, a need to integrate CDTI with health education on the importance of ivermectin uptake.