This review offers a comprehensive examination of the role of microglia in the pathogenesis of autoimmune uveitis, an inflammatory eye disease with significant potential for vision impairment. Central to our discussion is the dual nature of microglial cells, which act as both protectors and potential perpetrators in the immune surveillance of the retina. We explore the mechanisms of microglial activation, highlighting the key signaling pathways involved, such as NF-κB, JAK/STAT, MAPK, and PI3K/Akt. The review also delves into the genetic and environmental factors influencing microglial behavior, underscoring their complex interaction in disease manifestation. Advanced imaging techniques and emerging biomarkers for microglial activation, pivotal in diagnosing and monitoring the disease, are critically assessed. Additionally, we discuss current and novel therapeutic strategies targeting microglial activity, emphasizing the shift towards more precise and personalized interventions. This article aims to provide a nuanced understanding of microglial dynamics in autoimmune uveitis, offering insights into potential avenues for effective treatment and management.