The aim of this study was to perform a systematic review and meta-analysis of randomized controlled trials (RCTs) or cohort studies that evaluated the effect of aerobic endurance exercise on pulse wave velocity (PWV) and intima media thickness (IMT) in adults. IMT and PWV were the most commonly used parameters for the assessment of arterial stiffness. The MEDLINE, Cochrane, ISI, and Ovid databases were searched between January 2000 and February 2015. A total of 1654 participants in 26 RCTs and two cohort studies were included in the meta-analysis. In studies for which PWV was the outcome, aerobic endurance exercise had a significant effect on reducing PWV [-0.67, 95% CI -0.97, -0.38; I(2) = 89%; heterogeneity, P < 0.0001]. Changes in peripheral arterial PWV were statistically greater than in central arterial PWV. In the RCTs for which IMT was the outcome, changes [-0.04, 95% CI -0.12, 0.04; I(2) = 95%; heterogeneity, P < 0.00001] in IMT did not reach statistical significance. In the two cohort studies, changes [-8.81, 95% CI -9.25, -8.37; I(2) = 22%; heterogeneity, P = 0.26] in IMT were statistically significant. Subgroup analysis indicated a longer duration aerobic exercise and a greater improvement in VO2max were associated with larger reductions in PWV. Reductions in IMT were observed in two cohort studies, but not in four RCTs.