Background: Atrial fibrillation (AF) is associated with death in patients with chronic kidney disease (CKD). We examined the associations between AF and cause-specific mortality in a large CKD population. Methods: We included 62,459 patients with estimated glomerular filtration rate 15–59 mL/min/1.73 m2 (6,639 patients with AF and 55,820 without AF) followed in a large health care system. Outcomes included overall and cause-specific deaths (a) cardiovascular; (b) malignancy; and (c) non-cardiovascular/non-malignancy causes. Cox regression models for overall mortality and separate competing risk models for each major cause of death category were used to evaluate their respective associations with AF. Results: During a median follow-up of 4.1 years, 19,094 patients died; cause of death was known for 18,854 patients. After multivariable adjustment (demographics, comorbidities, relevant laboratory data, medication use, and kidney function), AF was associated with 23% (95% CI 18–29%) higher risk of all-cause mortality, 45% (95% CI 31–61%) higher risk of cardiovascular mortality and 13% (95% CI 3–22%) lower risk of malignancy-related mortality. Exclusion of patients with malignancy yielded similar results except for a lack of association between AF and malignancy-related deaths. Results were consistent across various stages of CKD. Conclusions: In a non-dialysis-dependent CKD population, the presence of AF was associated with higher all-cause and cardiovascular mortality. These data suggest that patients with both CKD and AF are at high cardiovascular risk, and thus clinical practice (or trials) should aim at reducing the overall excess cardiovascular mortality (not stroke alone) in patients with AF and CKD.