Background: In Sub-Saharan Africa, most nutrition efforts have concentrated on under-nutrition in children. However, national surveys rarely report the high prevalence of overweight and obesity among children. Likewise, in Ethiopia there is growing recognition of the emergence of a “double-burden” of malnutrition, with under and over nutrition occurring simultaneously among children, especially allied with improvements in socio-economic conditions. Hence, the study aimed to assess the prevalence and factors associated with overweight and obesity among private kindergarten school children aged 3-6 years in Bahirdar town, Northwest Ethiopia. Methods: A school-based cross sectional study was conducted in Bahirdar Town, northwest Ethiopia from August to September, 2015. Anthropometric measurements such as weight and height were taken from 462 private Kindergarten preschool children aged 3-6 years; socio-economic and demographic factors and feeding practices were collected by interviewing the, mothers or caregivers of the children. The z-score values for BMI-for-age of children were generated using Emergency Nutrition Assessment (ENA) for Standardized Monitoring and Assessment of Relief Transitions (SMART) 2011. Binary logistic regression model was used to identify factors associated with overweight and obesity in children. Odds ratio with 95% confidence interval (CI) was calculated to show the strength of association. Results: The overall prevalence of overweight and obesity was 6.9% [95% CI 2.4, 11.4]. The prevalence of overweight and obesity were 4.1 and 2.8%, respectively. The odds of overweight and obesity was higher among children with high dietary diversity score (DDS) [AOR = 5.12, 95% CI 1.42, 18.47], family size of less than five [AOR = 4.76, 95% CI 1.84, 12.31] and a family having a private car [AOR = 3.43, 95% CI 1.02, 11.49]. Conclusions: The prevalence of overweight and obesity among private kindergarten preschool children in the study area was high. Interventions on improving feeding practice and doing physical activities are important for the control of overweight and obesity among children in urban settings.