Purpose In patients with early gastric cancer (EGC) who undergo endoscopic submucosal dissection (ESD) with endoscopic curability (eCura) C-2, the risk of non-gastric cancer mortality should be evaluated before receiving further gastrectomy. Charlson comorbidity index (CCI) is often used to estimate prognosis based on patient's background before treatment. We identified the long-term risk of mortality from other causes associated with comorbidities in CCI and applied it to the creation of EGC specific CCI (GCCI). Methods A total of 1810 patients with EGC from 3 centers were included from January 2015 to February 2023. We used Cox proportional risk models to determine the risk of non-gastric cancer mortality related to comorbidities and used these hazard ratios to reweight the Charlson index to establish GCCI. Results The Cox model suggested that moderate to severe liver disease, metastatic solid tumors, severe to very severe chronic obstructive pulmonary disease (COPD), and leukemia had the highest risk of non-gastric cancer mortality [hazard ratio (HR) > 5)]. Survival analysis showed that the 5-year non-gastric cancer mortality rates in low-risk group (GCCI score 0-1), medium-risk group (GCCI score 2-4), and high-risk group (GCCI score 5-13) were 3%, 10%, and 52%, respectively. Conclusions GCCI could identify patients with EGC who have higher non-gastric cancer mortality. The GCCI could be used to help patients with EGC make medical decisions.