Abstract Background The total number of resected lymph nodes (LNs) is an important determinant of longer survival after esophagectomy for esophageal squamous cell carcinoma (ESCC). However, resected LN counts from which areas affect long-term outcomes remain unclear. Methods: This study comprised 406 patients who underwent minimally invasive esophagectomy (MIE) at Kobe University Hospital. Resected LN counts were evaluated in the following areas: upper mediastinal (UM), middle mediastinal (MM), lower mediastinal (LM), and abdominal (Abd). Cut-off values for LN counts from each area were determined using receiver operating characteristics analysis to the survival status. Cox proportional hazards regression analyses were performed to identify prognostic factors. Results: The cut-off values for large or small numbers of resected LN counts in the UM, MM, LM, and Abd areas were 4, 8, 5, and 18 in patients with upper and middle thoracic (Ut/Mt) ESCC, respectively, and 7, 6, 5, and 24 in patients with lower thoracic (Lt) ESCC, respectively. Multivariate analysis in patients with Ut/Mt ESCC revealed that tumor invasion depth, lymph node metastasis and the resected LN count from the UM area were independent risk factors for overall survival (hazard ratio = 7.04; 95% confidence interval = 4.47-11.1, hazard ratio = 4.01; 95% confidence interval = 1.96-8.21, hazard ratio = 2.18; 95% confidence interval = 1.24-3.82, respectively). In patients with Lt ESCC, tumor invasion depth, lymph node metastasis and pulmonary complication were independent risk factors for overall survival (hazard ratio = 4.23; 95% confidence interval = 2.14-8.35, hazard ratio = 3.83; 95% confidence interval = 1.75-8.38, hazard ratio = 2.80; 95% confidence interval = 1.38-5.65, respectively). Resected LN counts from no areas were prognostic factors. Conclusions: The number of resected LNs from the UM area influenced survival outcomes of patients with Ut/Mt ESCC after MIE.