Abstract Background Recently, the incidence of gastroesophageal junction (GEJ) cancer has been increasing in Eastern countries. Mediastinal lymph node (MLN) metastasis rates among patients with GEJ cancer are reported to be 5–25%. However, survival benefits associated with MLN dissection in GEJ cancer has been a controversial issue, especially in Eastern countries, due to its rarity and potential morbidity. Methods We retrospectively reviewed 290 patients who underwent surgery for GEJ cancer at the National Cancer Center in Korea from June 2001 to December 2015. Clinicopathologic characteristics and surgical outcomes were compared between patients without MLN dissection (Group A) and patients with MLN dissection (Group B). Prognostic factors associated with the survival rate were identified in a multivariate analysis. Results Twenty-nine (10%) patients underwent MLN dissection (Group B). Three of 29 patients (10.3%) showed a metastatic MLN in Group B. The 5-year disease-free survival rate was 79.5% in Group A and 33.9% in Group B (P < 0.001). The multivariate analysis revealed that abdominal LN dissection, pT category, and pN category were statistically significant prognostic factors. LNs were the most common site for recurrence in both groups. Conclusion Abdominal LN dissection and pathologic stage are the important prognostic factors for type II and III GEJ cancer rather than mediastinal lymph node dissection.