The relationship between ultra-processed food (UPF) intake and mortality is unknown in Asian countries, yet the intake of UPF is on the rise in these countries. This study examined the association of UPF intake with all-cause, cancer and cardiovascular disease (CVD) mortality. Participants were 113,576 adults who responded to a 106-item food frequency questionnaire during recruitment of the 2004–2013 Health Examinees (HEXA) study, a prospective cohort study in Korea. UPF were defined using the NOVA classification and evaluated as quartiles of the proportion of UPF in the diet (% total food weight). Multivariable Cox regression and restricted cubic spline models were used to examine the association of UPF intake with all-cause and cause specific mortality. A total of 3456 deaths were recorded during a median follow-up of 10.6 (interquartile range, 9.5–11.9) years. There was no evidence of an association of UPF intake with all-cause, cancer or CVD mortality comparing the highest with the lowest quartiles of UPF intake (all-cause mortality, men: hazard ratio [HR] 1.08, 95% confidence interval [CI] 0.95–1.22; women: HR 0.95, 95% CI 0.81–1.11; cancer mortality, men: HR 1.02, 95% confidence interval [CI] 0.84–1.22; women: HR 1.02, 95% CI 0.83–1.26; CVD mortality, men: HR 0.88, 95% CI 0.64–1.22; women: HR 0.80, 95% CI 0.53–1.19). However, the risk of all-cause mortality increased in both men and women with high consumption of ultra-processed red meat and fish (men, HR 1.26, 95% CI 1.11–1.43); women, HR 1.22 95% CI 1.05–1.43); and in men with high consumption of ultra-processed milk (HR 1.13, 95% CI 1.01–1.26); and soymilk drink (HR 1.12, 95% CI 1.00–1.25). We found no evidence of an association between total UPF intake and all-cause, cancer or CVD mortality, but ultra-processed red meat and fish in both sexes, and milk and soymilk drinks in men were positively associated with all-cause mortality.