The aims of this study were (a) to compare the clinical presentations and outcomes of patients referred to the hospital from the emergency department (ED) and those referred from non-ED facilities in a Chinese population and (b) to identify the factors influencing delays in medical assessment and prognosis for patients with rectal cancer (RC). Eligible Chinese patients newly diagnosed with RC, admitted to the hospital from the ED, or referred from non-ED sources between 1 January 2008 and 31 December 2009 were enrolled in this prospective study. Associations between symptoms, symptom duration, tumor stage at diagnosis, and 3-year survival were proposed to identify factors associated with delay in the diagnosis of RC and emergency admission. Compared with patients in the non-ED group, patients in the ED group had a significantly longer hospital stay, greater in-hospital mortality, a higher proportion of advanced stage tumor, lower rate of undergoing potentially curative surgery, and a higher proportion of symptom duration longer than 1 month. There was a statistically significant difference in the 3-year overall survival between the patients who underwent emergency operation within 24 h of admission and the patients presenting as emergency who underwent an operation longer than 24 h from admission to operation. Patients who endured symptoms longer than 1 month had a significantly higher proportion of emergency admissions, higher proportion of advanced stage tumor, and lower rate of undergoing potentially curative surgery compared with patients whose symptom duration was less than 1 month. In conclusion, (a) ED referral patients endured significantly longer symptom duration before diagnosis. (b) Emergency operation within 24 h of admission was an independent prognostic indicator of overall survival in patients with RC. A two-stage approach for the management of patients with RC who presented as emergency could enable patients to be transferred to a specialist department of surgical oncology for a definitive radical oncological operation and improve the prognosis.