Objective We reviewed data pertaining to fenestrated endograft technique and chimney stent repair of complex aortic aneurysm for comparative analysis of the outcomes. Methods A comprehensive search of relevant databases was conducted to identify articles in English, related to the treatment of complex aortic aneurysm with fenestrated endovascular aneurysm repair and chimney stent repair, published until January 2015. Results A total of 42 relevant studies and 2264 patients with aortic aneurysm undergoing fenestrated endovascular aneurysm repair and chimney stent repair were included in our review. A total of 4413 vessels were involved in these processes. The cumulative 30-day mortality was 2.4% and 3.2% (p=0.459). The follow-up aneurysm-related mortality was 1.4% and 3.2% (p=0.018), and target organ dysfunction was 5.0% and 4.0% in fenestrated endovascular aneurysm repair and chimney stent repair, respectively (p=0.27). A total of 156 vessels showed restenosis or occlusion after primary intervention (3.6% and 3.4% in fenestrated endovascular aneurysm repair and chimney stent repair, respectively, p=0.792). The cumulative type I endoleak was 2.0% (38/1884) after fenestrated endovascular aneurysm repair compared with 3.4% (13/380) after chimney stent repair (p=0.092), and the type II endoleak was 5.4% (102/1884) and 5.3% (20/380), respectively (p=0.905). Approximately, 1.1% and 1.6% increase in aneurysm was observed following fenestrated endovascular aneurysm repair and chimney stent repair, respectively (p=0.437). The re-intervention frequency was 205 and 19 cases after fenestrated endovascular aneurysm repair and chimney stent repair, respectively (11.7%, 5.6%, p=0.001). Conclusions Fenestrated endovascular aneurysm repair and chimney stent repair are safe and effective in treating patients with complex aortic aneurysm. A higher aneurysm-related mortality was observed in chimney stent repair while fenestrated endovascular aneurysm repair was associated with a higher re-intervention rate.