Uveitis causes blindness and critical visual impairment in people of all ages, and retinal microglia participate in uveitis progression. Unfortunately, effective treatment is deficient. Icariin (ICA) is a bioactive monomer derived from Epimedium. However, the role of ICA in uveitis remains elusive. Our study indicated that ICA alleviated intraocular inflammation in vivo. Further results showed the proinflammatory M1 microglia could be transferred to anti-inflammatory M2 microglia by ICA in the retina and HMC3 cells. However, the direct pharmacological target of ICA is unknown, to this end, proteome microarrays and molecular simulations were used to identify the molecular targets of ICA. Data showed that ICA binds to peroxiredoxin-3 (PRDX3), increasing PRDX3 protein expression in both a time- and a concentration-dependent manner and promoting the subsequent elimination of H2O2. In addition, GPX4/SLC7A11/ACSL4 pathways were activated accompanied by PRDX3 activation. Functional tests demonstrated that ICA-derived protection is afforded through targeting PRDX3. First, ICA-shifted microglial M1/M2 phenotypic polarization was no longer detected by blocking PRDX3 both in vivo and in vitro. Next, ICA-activated GPX4/SLC7A11/ACSL4 pathways and downregulated H2O2 production were also reversed via inhibiting PRDX3 both in vivo and in vitro. Finally, ICA-elicited positive effects on intraocular inflammation were eliminated in PRDX3-deficient retina from experimental autoimmune uveitis (EAU) mice. Taking together, ICA-derived PRDX3 activation has therapeutic potential for uveitis, which might be associated with modulating microglial M1/M2 phenotypic polarization.