Objective: This study compared the long-term prognosis of endoscopic submucosal dissection (ESD) versus surgical treatment in patients with early Siewert type II adenocarcinoma of the esophagogastric junction (AEGJ). Methods: A retrospective analysis was conducted on 562 patients with early Siewert type II AEGJ who underwent ESD or radical surgery at a single tertiary hospital between January 2010 and February 2021, including 393 patients treated with ESD and 169 with surgery. Propensity score matching (PSM) was applied to balance baseline characteristics. Kaplan-Meier analysis was used to compare long-term survival outcomes between the two groups. Results: Among the 562 patients, 393 received ESD and 169 underwent surgery, with a median follow-uP of 57.7 months (range: 6.2–147 months). After PSM, two balanced cohorts of 163 patients each were generated. The 5-year overall survival (OS) rates showed no significant difference between the ESD and surgery groups (92.5% vs. 90.7%, P = 0.734). Similarly, no significant differences were observed in OS (P = 0.95) or disease-specific survival (P = 0.18) between the two groups. The analysis of adverse events showed no significant differences between the two groups in lymph node metastasis (6.7% vs. 7.4%, P = 0.829), local recurrence (4.9% vs. 9.2%, P = 0.130), postoperative stenosis (3.7% vs. 1.2%, P = 0.152), or bleeding (1.2% vs. 0.6%, P = 0.562). However, the incidence of acid reflux symptoms was significantly higher in the surgery grouP (11.0% vs. 3.1%, P = 0.005). Conclusion: Early Siewert type II AEGJ patients treated with ESD or surgery demonstrated comparable long-term survival outcomes, supporting the role of ESD as a viable therapeutic option for this population.