Background: Neoadjuvant chemoradiotherapy (NACRT) has become a widely accepted strategy for rectal cancer (RC). The purpose of this study is to examine the safety and efficacy of a novel protocol of neoadjuvant hyperfractionated short-course radiotherapy (NAHSRT) combined with chemotherapy for locally advanced RC. Methods: 82 patients (pts) with RC were treated with NACRT followed by radical surgery between March 2008 and May 2012. 50 pts with RC of cT3N1M0 were analyzed in the present study. NAHSRT was performed with a dose of 2.5 Gy twice daily, with an interval of at least 6 hours between fractions, up to a total dose of 25 Gy (25 Gy in 10 fractions for 5 days) with chemotherapy. Radical surgery was performed within 3 week following the end of the NAHSRT. Results: 50 pts included 37 men and 13 women. The median age was 65.0 (range: 39-85) years. The median follow-up term was 12.0 (2-36) months. S-1, oxaliplatin with capecitabine, and fluorouracil, leucovorin plus irinotecan (FOLFIRI) was administered with NAHSRT in 48 pts, 1 pt, and 1 pt, respectively. 48 pts (96%) had no apparent adverse events before surgery. 49 pts (98%) completed NACRT except for 1 pt stopped chemotherapy (S-1) because of grade 3 gastrointestinal toxicity (CTCAE v.3). In addition, no pts showed grade 4 toxicities. Postoperative complications were found in 30 pts (60.0%). 33 pts (66.0%) received adjuvant chemotherapy. S-1, capecitabine, oxaliplatin with capecitabine, uracil/tegafur (UFT) and oral leucovorin, and oxaliplatin combined with S-1 (SOX) was delivered after surgery in 20 pts, 4 pts, 4 pts, 4 pts, and 1 pt, respectively. No pts. developed local failure, although distant failures were found in 3 pts. The median disease free survival and overall survival was 11.6 (2-36) months and 12.0 (2-36) months, respectively. In addition, disease-specific survival rate was 100.0%. Conclusions: We presented a novel protocol of NAHSRT for locally advanced RC and the short-term outcome. NAHSRT was well tolerated and produced excellent short-term outcomes in pts with locally advanced RC.