Abstract Background Few studies have examined gender differences in the clinical management of rectal cancer. We examine differences in stage at diagnosis and preoperative radiotherapy in rectal cancer patients. Methods A prospective cohort study was conducted in 22 hospitals in Spain including 770 patients undergoing surgery for rectal cancer. Study outcomes were disseminated disease at diagnosis and receiving preoperative radiotherapy. Age, comorbidity, referral from a screening program, diagnostic delay, distance from the anal verge, and tumor depth were considered as factors that might explain gender differences in these outcomes. Results Women were more likely to be diagnosed with disseminated disease among those referred from screening (odds ratio, confidence interval 95% (OR, CI = 7.2, 0.9–55.8) and among those with a diagnostic delay greater than 3 months (OR, CI = 5.1, 1.2–21.6). Women were less likely to receive preoperative radiotherapy if they were younger than 65 years of age (OR, CI = 0.6, 0.3–1.0) and if their tumors were cT3 or cT4 (OR, CI = 0.5, 0.4–0.7). Conclusions The gender-specific sensitivity of rectal cancer screening tests, gender differences in referrals and clinical reasons for not prescribing preoperative radiotherapy in women should be further examined. If these gender differences are not clinically justifiable, their elimination might enhance survival.