The present study tested our hypothesis that university students with irritable bowel syndrome (IBS) may experience less satisfactory academic lives than those of students without IBS. We also verified the hypothesis that university students with IBS might have higher employment anxiety than students without IBS might. We conducted a cross-sectional study of 1,686 university students. Presence or absence of IBS was assessed via the Rome III Questionnaire. Two original items were used to evaluate academic life. The prevalence rates of IBS with diarrhea, IBS with constipation, mixed IBS, and unsubtyped IBS in the study population were 5%, 2%, 10%, and 3%, respectively. Regarding academic life, the proportions of participants who experienced maladjustment and employment anxiety were 29% and 50%, respectively. After adjusting for age, sex, and faculty, the odds ratios for maladjustment and employment anxiety were significantly higher in students who screened positively, relative to those who screened negatively, for IBS (OR, 1.62; 95% CI, 1.24–2.21; OR, 2.16; 95% CI, 1.68–2.81, respectively). In conclusion, maladjustment and anxiety over future employment were higher in university students with IBS relative to those without.