Background Esophagogastric junction (EGJ) cancers are resected thorough esophagectomy or gastrectomy, with the incidence of postoperative complications influenced by the chosen procedure. Methods In this prospective nationwide multicenter study, patients with cT2-T4 EGJ cancers were enrolled before surgery. Based on the protocol, surgeons performed a transthoracic esophagectomy (TTE) or a transhiatal gastrectomy (THG) and dissected all lymph nodes prespecified as the standardized procedure. Postoperative complications were correlated with the clinical factors in each procedure. Results A total of 345 patients were eligible for this study. TTE and THG were performed in 120 and 225 patients, respectively. Complications of Clavien-Dindo ≥ Grade II were found in 115/345 (33.3%) patients. Recurrent laryngeal nerve palsy was found only in the TTE group (p < 0.001). The incidence of other complications was not significantly different between the two groups. High body mass index (BMI) in the TTE group, male sex, and longer esophageal invasion in the THG group were significantly correlated with complications ≥ Grade II (p = 0.049, 0.037, and 0.019, respectively). Anastomotic leakage was most frequently observed (12.2%). Tumor size in the THG group (p = 0.02) was significantly associated with leakage. All six patients with ≥ Grade IV leakage underwent THG, whereas, none of the patients in the TTE group had leakage ≥ Grade IV (2.7% vs. 0%, p = 0.096). Conclusions Surgical resection should be performed with utmost care, particularly in patients with a high BMI undergoing TTE, and in patients with larger tumors, longer esophageal invasion, or male patients undergoing THG.