Background Neoadjuvant therapy followed by surgery can improve long-term survival and reduce local recurrence in patients with esophageal squamous cell carcinoma (ESCC). Extracapsular lymph node involvement (ECLNI) reflects tumor progression in gastrointestinal malignancies. The aim of this study was to clarify the correlation between ECLNI and clinical outcome in ESCC following neoadjuvant therapy. Methods A total of 36 patients with ESCC who underwent neoadjuvant therapy followed by surgery were enrolled in this study (CT: n = 16; CRT: n = 20). The correlation between ECLNI and clinicopathological variables was investigated. In addition, we also evaluated whether differences in pathological response existed between primary tumors and metastatic lymph nodes (LNs), and whether chemotherapy (CT) and chemoradiotherapy (CRT) had different effects on LNs. Results Of 36 patients, 22.2 % had detectable ECLNI. ECLNI was significantly correlated with tumor size (> 40 mm), LN density (a parts per thousand 20 %), advanced stage, lymphatic invasion, non-R0 resection, and poor pathological response. Patients with ECLNI had a significantly poorer prognosis than those without ECLNI (P = 0.0040). No differences in pathological response were observed between primary tumors and metastatic LNs for each type of therapy. The median number of dissected LNs was 21, 45, and 14 in the surgery alone (n = 22), CT, and CRT groups, respectively (P < 0.05). More severe morphologic changes in LNs appeared to be induced by CRT than by CT. Conclusion ECLNI was correlated with poor prognosis in patients with ESCC after neoadjuvant therapy. CT and CRT had different effects on LNs.