Objective: Numerous previous studies have suggested that physical activity or exercise may play an important role in both structural integrity of the brain and cognitive function. However, it is unclear what effect exercise has on cognitive related brain structure. The present study comprehensively reviews the effect of exercise on cognitive related brain regions of the healthy elderly by using activation likelihood estimation (ALE). Materials and methods: Seven electronic databases were searched for randomized controlled trials published up to September 2017. The quality of the selected studies was evaluated using the Cochrane Collaboration's tool for assessing the risk of bias. GingerALE version 2.3.6 was used to perform the coordinate-based ALE meta-analysis. Results and conclusions: Nine randomized controlled trials (RCTs) with 50 distinct foci were analyzed for structural changes, containing 412 healthy older subjects. ALE showed significant regional increases in regions including the left superior temporal gyrus, left medial temporal gyrus, left inferior frontal gyrus, right medial frontal gyrus, right and left superior frontal gyrus, left cingulate gyrus, right anterior cingulate and left lentiform nucleus in subjects with the exercise intervention compared to controls. However, considering the quantity and limitations of the included studies, the conclusion could not yet be drawn. Additional randomized controlled trials with rigorous designs and longer intervention periods are needed in the future.