Current studies have not clarified the relationship between riboflavin intake and all-cause mortality in patients with chronic kidney disease (CKD). The aim of this study is to investigate whether there is an association between riboflavin intake and the risk of all-cause mortality in patients with CKD. This was a retrospective cohort study with data extracted from the National Health and Nutrition Examination Survey (NHANES). The study was conducted using Cox regression analysis to calculate hazard ratio (HR) and 95% confidence interval (CI) to assess the association between riboflavin intake and risk of all-cause mortality. Subgroup analyses were performed regarding gender, CKD stage, hypertension, hyperlipidemia and cardiovascular disease (CVD). A total of 3750 patients were ultimately included in the analyses. After excluding potential confounders, lower intake of riboflavin was associated with the higher risk of all-cause mortality (Q1: HR = 1.33, 95% CI: 1.05-1.69). The similar association was also found in patients at mild/moderate stage (HR = 1.32, 95% CI: 1.05-1.66), in female (HR = 1.35, 95% CI: 1.01-1.81), with hypertension (HR = 1.37, 95% CI: 1.07-1.75), CVD (HR = 1.48, 95% CI: 1.08-2.03), and dyslipidemia (HR = 1.29, 95% CI: 1.01-1.66). This study found the association between low riboflavin intake and high risk of all-cause mortality, indicating a potential beneficial role of riboflavin in CKD patients.