The purpose of this study is to examine the appropriateness of MRI navigation surgery following chemoradiotherapy (CRT), including lateral pelvic lymph node dissection (LLND) for middle to low rectal cancer. Forty-three consecutive patients with cT2-4b rectal cancer within 10 cm from the anal verge who underwent laparoscopic radical surgery following CRT (45–50.4Gy + S1 80mg/m2) from January 2014 and February 2020 were analyzed. We decided on the operative procedure, including LLND, based on the restaging MRI. We examined the rates of 3-year postoperative local pelvic recurrence, permanent stoma, and recurrent risk factors (Group S). We also compared the results to that of the fourteen patients who enrolled in the previous phase II trial and underwent laparoscopic radical surgery following CRT (40Gy + S-1 (80mg/m2) or UFT (300 mg/m2)) for consecutive cT2-4b rectal cancer below the peritoneal reflection. The operative procedure was decided at the initial MRI diagnosis, and the LLND was not performed (Group P). We had no local pelvic recurrence in Group S, and the three-year local pelvic recurrence-free survival was significantly better in Group S than P (100 % in S 85.1 % in P, p < 0.05). The permanent stoma rate was not different between the Groups, irrespective of the significantly high rate of cCRM(+) in Group S. The Cox proportional hazards model for significant factors of recurrence on the univariate analysis revealed that ycM and ycEMVI scores were independently significant (p < 0.001). MRI navigation surgery, including LLND for rectal cancer following chemoradiotherapy, improves local control and functional preservation. •CRT does not compensate for the lateral lymph node dissection.•Selective TME and selective LLND following CRT improve local control and functional preservation.•ESGAR ‘s metastatic lymph node diagnostic criteria helped differentiate patients requiring LLND.•MRI navigation surgery can be based on ycCRM and metastatic LLN diagnosis.