Abstract Introduction Admission to university influences lifestyle behaviors and is marked by a daily routine of accumulation of activities that can interfere with sleep duration, affecting food choices and meal consumption habits throughout the day. Objective To analyze the association between short sleep duration and skipping main meals among university students. Materials and Methods We conducted a cross-sectional study with 1,608 university students aged between 16 and 25 years, who were enrolled in full-time undergraduate courses at a public university in the Midwestern region of Brazil. Information on skipping breakfast, lunch, and dinner was collected through the question “On average, how often do you eat the following meals?”. Given the lack of a uniform criterion to define “skipping a meal”, in the present study, any answer that did not correspond to the daily consumption of the meal was classified as meal skipping, based on the recommendation of the Dietary Guidelines for the Brazilian Population. Short sleep duration was determined according to sleep time during the night (≤ 6 hours for those aged ≥18 years and ≤ 7 hours for those under 18 years of age). Associations were estimated using adjusted Poisson regression models. Results The prevalences of skipping breakfast, lunch, and dinner were of 51.0%, 13.9%, and 35.6% respectively. Short sleep duration was observed in 27.2% of the study population. After adjusting for confounding variables, short sleep duration was positively associated with skipping breakfast (adjusted prevalence ratio [PRadj] = 1.20; 95% confidence interval [95%CI] = 1.08–1.34) and skipping lunch (PRadj = 1.64; 95%CI = 1.27–2.12). Conclusion University students presented a high prevalence of skipping main meals. Short sleep duration was directly associated with skipping two major meals of the day: breakfast and lunch.