Irritable bowel syndrome (IBS) is a common recurrent functional gastrointestinal disorder that impacts on patients physically and mentally. Studies on IBS have focused on adults, yet few studies have examined IBS among female university students. The aim of this study was to investigate the prevalence of IBS for female university students and its related factors. Using a cross-sectional study design, a total of 2520 female university students were recruited in southern Taiwan. The structured questionnaires, including the Rome III IBS diagnostic questionnaire, IBS symptom severity scale, Perceived Stress Scale, and World Health Organization Quality of Life BREF questionnaire (WHOQOL-BREF) were used for data collection. A total of 1894 female students complete the questionnaires. The response rate was 75.15%. The results indicated 193 female students with IBS and the prevalence of IBS was 10.1%. IBS female students had higher levels of stress and lower QOL than non-IBS female students. The risk factors for female university students developing IBS were dysmenorrhea, food avoidance, class absenteeism, and the lower physical domain of QOL. It is advised to consider these factors when providing students with counselling and relevant services in the expectation of alleviating their IBS symptoms, reducing the incidence rate of IBS, and further improving their QOL.