The reduced effectiveness of some of the most important antibiotics owing to increasing resistance of microorganisms as well as the absence of new classes of antimicrobial agents have been concerning researchers and clinicians in recent years. Thus, the development and approval of new compounds for clinical applications is of great importance. Among these compounds, antimicrobial peptides (AMPs) appear to be excellent candidates for the development of novel antimicrobial agents. Some AMPs and antimicrobial proteins have been shown to be active against relevant pathogens in ocular infections as well as in biofilm eradication from contact lenses. Thus, they are considered promising in the prevention and management of ocular diseases. This review summarises the main classes and characteristics of AMPs and antimicrobial proteins, in particular those found in ocular structures and fluids. Some AMPs with activity against ocular pathogens and their potential as therapeutic agents to treat and prevent ocular infections are emphasised.