Objective Recent epidemiological evidence indicates an association between chronic kidney disease (CKD) and the risk of new-onset atrial fibrillation (AF), but the results are inconclusive. This meta-analysis examined the association between CKD and new-onset AF. Methods PubMed, EMBASE, the Cochrane Collaboration and the reference lists of relevant articles were searched to identify eligible studies. The random effect model was used to calculate the overall multivariable-adjusted hazard ratio (HR) with its corresponding 95% confidence interval (CI). Associations were tested in subgroups of study characteristics and study quality criteria. We also performed sensitivity analyses and assessments of publishing bias. Results Seven prospective cohort studies (n = 400,189 participants) were included in this meta-analysis. Pooled results suggested that CKD was associated with an increased adjusted risk estimate for new-onset AF (HR, 1.47; 95% CI, 1.21-1.78), with significant heterogeneity between these studies (I-2 = 79.7%, P<0.001). Results were not different in any subgroup except sample size. Stratified analyses found that the diagnostic method of CKD and eGFR (estimated glomerular filtration rate), the number of confounders adjusted for, and study quality explained little of the variation between studies. Sensitivity analysis further demonstrated the results to be robust. Conclusions CKD is associated with an increased risk of incident AF. Further research is needed to investigate the biological association between CKD and AF and identify a preventive strategy to decrease the incidence of AF in CKD patients.