Abstract Background Intestinal parasitic infections are still common in low-income countries including Ethiopia, particularly in children due to low-quality drinking water, poor personal and environmental sanitation. Disabled individuals are excluded from most academic, economic, social and cultural opportunities, they are among the poorest and most marginalized of the whole world’s people. The aim of this study was to assess the prevalence of intestinal parasitic infections and associated factors among mentally disabled and non-disabled students at primary schools in Bahir Dar city, Amhara regional state, Ethiopia, 2018. Methods A school-based Comparative cross-sectional study design was conducted from November 1–30, 2018. A total of 418 study participants, 104 mentally disabled and 314 non-disabled students were recruited through a simple random sampling technique. The collected data were coded, entered and cleaned with EpiData version 3.1 and analyzed using SPSS version 23. Multivariable logistic regression was conducted to identify factors associated with intestinal parasitic infections. The adjusted odds ratio with a 95% Confidence interval at a 5% level of significance was used to measure the strength of association. Results The mean age of study participants was 14.05 ± 3.66 and 11.96 ± 2.94 for mentally disabled students and non-disabled students. Prevalence of parasitic infection was 56.70% (n = 59) for mentally disabled students whereas 41.10%(n = 129) for non-disabled students. Unclean fingernails [AOR = 2.42; 1.40,4.17], health checkups [AOR = 1.87;1.16,3.02], hand washing with water only [AOR = 2.48; 1.49,4.12], cooking and sanitation source of water [AOR = 4.40;2.32,8.36], Grade [ (1–4)] [AOR = 2.27;1.41,3.67], sex [AOR = 1.64;1.03,2.63] and Family size> = 7 [AOR = 2.74;1.25,5.99] were variables which showed statistically significant association with intestinal parasitic infections. Conclusion The prevalence of intestinal parasitic infection was higher among mentally disabled students than non-disabled students. Unclean fingernails, health checkups, hand washing habits, source of water, family size, sex and Grade of students have had a statistically significant association with intestinal parasitic infections. Periodic medicinal treatment was needed twice a year for mentally disabled and once a year for non-disabled students.