Background Endoscopic submucosal dissection (ESD) is an endoscopic alternative to surgical resection of early gastric cancer (EGC). Besides offering both diagnostic and therapeutic capability, it has the benefits of reducing post-operative complications and provides fast recovery and better quality of life compared to surgical resection of neoplastic lesions. However, due to limitations of the procedure, its long-term outcomes are rather controversial. Methods This study has been carried out to investigate the long-term outcomes of ESD which includes the overall survival (OS), disease-free survival (DFS), and recurrence rate. The following databases were used to search for articles published until February 2018: Medline, Cochrane Library, PubMed, Web of Science, and EBSCO. Results A total of 13 eligible studies covering 4986 patients were selected for a meta-analysis based on specified inclusion and exclusion criteria. The difference of OS and disease-specific survival (DSS) between ESD and surgical treatment was not statistically significant (RR = 0.90, 95% CI = 0.68–1.19, p  = 0.46; RR = 0.40, 95% CI = 0.15–1.03, p  = 0.06, respectively). However, DFS in the ESD group was much lower than that in the surgery group (RR = 3.40, 95% CI = 2.39–4.84, p  < 0.001). In terms of the treatment after recurrence, the proportion of patients who could receive radical treatment was significantly higher in the ESD than that in the gastrectomy (OR = 5.27, 95% CI = 2.35–11.79, p  < 0.001). Conclusions This meta-analysis showed that ESD might be an alternative treatment option to surgery for patients with EGC in Asian countries. But a close surveillance program after ESD is of necessity, considering the higher possibility of tumor recurrence after ESD.