(1) Background: The Charlson comorbidity index (CCI) score has been shown to predict 10-year all-cause mortality, but its validity is a matter of debate in surgical patients. We wanted to evaluate CCI on predicting all-cause mortality in elderly patients undergoing emergency abdominal surgery (EAS); (2) Methods: This retrospective single center study included all patients aged 65 years or older consecutively admitted from January 2017 to December 2019, who underwent EAS and were discharged alive. CCI was calculated by using of the International Classification of Diseases, 9th Revision, Clinical Modification codes. Our outcome was all-cause death recorded during the 20.8 ± 8.8 month follow-up; (3) Results: We evaluated 197 patients aged 78.4 ± 7.2 years of whom 47 (23.8%) died. Mortality was higher in patients who underwent open abdominal surgery than in those treated with laparoscopic procedure (74% vs. 26%, p < 0.001), and in those who needed colon, small bowel, and gastric surgery. Mean CCI was 4.98 ± 2.2, and in subjects with CCI ≥ 4 survival was lower. Cox regression analysis showed that CCI (HR 1.132, 95% CI 1.009–1.270, p = 0.035), and open surgery (HR 10.298, 95%CI 1.409–75.285, p = 0.022) were associated with all-cause death independently from age and sex; (4) Conclusions: Calculation of CCI, could help surgeons in the preoperative stratification of risk of death after discharge in subjects aged ≥65 years who need EAS. CCI ≥ 4, increases the risk of all-causes mortality independently from age.