Background: The neutrophil-to-lymphocyte ratio (NLR) is considered an indicator of systemic inflammation and may predict prognosis in colorectal cancer. In this study, we examined the prognostic impact of NLR in patients with locally advanced low rectal cancer treated with neoadjuvant chemoradiotherapy (NACRT) followed by surgery. Methods: From 2004 to 2012, we analyzed 201 consecutive patients with locally advanced low rectal cancer below the peritoneal reflection who underwent NACRT and curative resection. Blood samples were obtained before NACRT. NLRs were dichotomized using a cut-off value of 3.0, which was chosen based on receiver operating characteristic analysis and previous studies, and we analyzed their relationship with clinical outcomes. Results: Forty-four (21.9%) patients had a high NLR. Moreover, a high NLR was significantly associated with elevated carcinoembryonic antigen levels before NACRT (p = 0.0154). Multivariate analysis showed that a high NLR was independently associated with worse overall survival (hazard ratio (HR) 3.38, p = 0.012). In contrast, a high NLR was not significantly associated with relapse-free survival (HR 1.073, p = 0.8438). The post-recurrence survival between patients with high and low NLRs was significantly different (p = 0.0370). Conclusions: A high NLR (≥3.0) prior to NACRT was independently associated with poor prognosis in patients with locally advanced low rectal cancer treated with NACRT and radical resection.