Chronic granulomatous disease (CGD) is a rare primary phagocytic immunodeficiency characterized by recurrent infections due to impaired NADPH oxidase activity. Balancing the need for additional immune suppression with the risk of infection in patients with CGD-associated inflammation can be difficult but increased understanding of the underlying pathophysiology may allow for more targeted and rational therapies. Current treatments for inflammatory complications include glucocorticoids, steroid-sparing immunosuppressive agents, antibiotics, and increasingly the use of targeted biologic agents. However, improved curative therapy strategies for patients with suboptimal donor options are needed and autologous gene therapy remains experimental.