Background: Trachoma is still the major public health problem in Amhara Region, Ethiopia. Intervention measures such as mass drug administration have been implemented to reduce the problem. However, the prevalence of trachoma and its associated factors have not yet investigated after the implementation of mass drug administration including promotion of facial cleanliness and environmental improvements. Objective: To assess prevalence and associated factors of active trachoma among children aged 1-9 years old in mass drug administration graduated and non-graduated districts in Central Gondar, Amhara Region Ethiopia. Methods: Comparative cross-sectional study was conducted from October 1, 2019 to November 15, 2019 in mass drug administration graduated and non-graduated districts. Stratified multistage sampling followed by systematic random sampling technique was used to select 690 households with children aged 1-9 years. Data was collected using a pretested questionnaire. Data was entered into Epi-data version 3.1 and exported to SPSS version 20.0 for analysis. Bivariate and multivariable logistic regressions were employed to identify factors associated with active trachoma. Crude and Adjusted Odds Ratio with 95% confidence interval were computed to assess the association between independent predictor and active trachoma. Result: The overall prevalence of active trachoma was 8.3% with 95% CI: 6.2% –10.5% and had shown significant variation (t-test P-value < 0.0001) between graduated 3.5% with 95% CI: 1.8% –5.6% and non-graduated (13.0%) with 95% CI: 9.7%–16.8% districts. Being lived in non-graduated districts (AOR= 6.165, 95% CI: 2.754, 13.800), fly presence in the house (AOR=3.158, 95% CI: 1.525, 6.540), Living together with more than two children aged 1-9 years old (AOR=3.672, 95% CI: 1.747, 7.717), did not wash face every day (AOR= 4.984, 95% CI:1.513, 16.416), did not use soap during washing of face (AOR= 2.930, 95% CI: 1.249, 6.874) and presence of sleep in eyes (AOR= 3.137, 95%CI: 1.420, 6.929) were identified as significant predictors of active trachoma (TF) among children aged 1-9 years old. Conclusion: The prevalence of active trachoma was high in the study area. Being lived in non-graduated districts, fly presence in the house, more than two children in a household, did not wash face every day, did not use soap during washing of face and presence of sleep in eyes were the significant predictors of active trachoma. Therefore, the identified modifiable factors are the area of intervention to reduce the burden of active trachoma. Key words: Active trachoma, Mass drug administration, graduated district, non-graduated district and Central Gondar zone.