Background: Mucosal esophageal squamous cell carcinoma (T1a EC) is treated with endoscopic (ER) or surgical resection (SR). The data regarding prognosis of T1a EC and the associated factors are still lacking. This study aimed to compare the treatment outcomes of T1a EC in ER and SR groups, and to investigate the factors affecting long-term survival. Methods: We retrieved data for 263 patients with T1a EC who underwent ER (n = 200) or SR (n = 63). Relevant clinical and tumor-specific parameters were reviewed. Underlying comorbidity was scored using Charlson co-morbidity index (CCI). Significant factors affecting survival were determined by Cox regression analysis. Results: The mean age of the patients was 64.5±8.0 years. During a mean follow-up of 54.4±20.4 months, the 5-year overall survival (OS) of all T1a EC patients was 85.7% (86.8% in ER and 82.4% in SR group; p = 0.631). In multivariate analysis, CCI was a significant factor affecting survival (p < 0.001). The 5-year OS was 60.2% in patients with CCI > 2 and 88.2% in patients with CCI ≤2 (p < 0.001). The 5-year cumulative incidence of primary EC recurrence was 1.9% and metachronous EC recurrence was 15.1% in ER group (0% in SR group). Incidence of subsequent second primary cancers was 9% in ER and 9.5% in SR. The 5-year cumulative incidences of all cases of cancer recurrence in ER and SR groups were 27.5% and 10.8%, respectively (p = 0.037). The procedure-related adverse events occurred in 10.0% in ER and 41.3% in SR (p < 0.001). Among the 24 (12.0%) and 10 (15.9%) deaths in ER and SR group, respectively, primary EC-specific death was not reported. The major causes of death were second primary cancers in ER group (75%), and post-operative complications or organ failure in SR group (70%). Conclusions: Long-term survival was excellent in patients undergoing ER or SR for T1a EC. The prognosis of T1a EC was significantly associated with underlying comorbidity. Attention should be paid to metachronous cancer recurrence in ER group and operation-related adverse events in SR group.