Background: Vitamin A deficiency (VAD) is one of the most prevalent micronutrient deficiencies in the world. About 2% of all deaths among children under five years of age (U-5) are attributable to VAD. Currently evidence-based knowledge is grossly lacking about the factors associated with low coverage of VAS. Objective: This study aims to determine the factors affecting low coverage of the vitamin A supplementation program among the young children admitted to a diarrheal hospital. Methods: We extracted data from the Diarrhoeal Diseases Surveillance System (DDSS) on children aged 12-59 months admitted to the Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh, from 1996 to 2014. A logistic regression model was constructed to identify the factors that were significantly associated with non-compliance to vitamin A supplementation (VAS). Strength of association was determined by calculating adjusted odds ratios (aORs) and their 95% confidence intervals. Results: A total of 8649 children were enrolled and comprised the analyzable sample. Their mean ± SD age was 25.2 ± 12.8 months and 40% were female. Around 68% of them had received VAS in the previous 6 months. In the logistic regression analysis, older (>24 months) children (aOR: 1.38; 95% CI: 1.24-1.53), having an illiterate mother (aOR: 1.43; 95% CI: 1.27-1.64), having an illiterate father (aOR: 1.3; 95% CI: 1.16-1.50), coming from the two lowest wealth quintiles (aOR:1.13; 95% CI: 1.02-1.27), with an average monthly household income <10,000 BDT, (1 USD = 60 BDT) and children who had not received the measles vaccine (aOR: 1.87; 95% CI: 1.63-2.19) were more likely not to have received VAS in the preceding six months. We also observed an increase in coverage of VAS from 61% to 76% over the last 18 years (p < 0.001). Conclusions: Non-compliance to VAS was found to be associated with older children, parents without formal schooling, family with greater poverty, low family income, and lack of measles vaccination. Specific programmatic approaches including prioritizing vulnerable children may enhance vitamin A coverage.