The complement system is a well-documented element of the immune system that protects the body from external pathogens. Although the majority of complement components are produced by the liver and secreted into the circulation, ocular tissues also produce several complement components, thereby contributing to local complement activity in specific regions of the eye. Regulation of complement cascade activation is crucial for preventing unintended cellular damage. In the alternative pathway of the complement system, complement factor H (CFH) plays an important role in inhibitory regulation. Certain genetic polymorphisms that result in defective CFH are associated with rare diseases where the self is attacked by an overactive complement system. This review will focus on the expression and localization of CFH in human ocular tissues and highlight its association with several diseases in the anterior and posterior chambers of the eye.