AIM: To test the therapeutic effects of delayed treatment of mesenchymal stem cells (MSCs) in recurrent experimental autoimmune uveitis (rEAU). METHODS: The efficacy of different regimens of MSC administration in rEAU were tested by evaluation of clinical and pathological intraocular inflammation, as well as retinal structural and functional integrity using optical coherence tomography (OCT) and electroretinogram (ERG). The retinal sections were also immunostained with antibodies to glial fibrillary acidic protein (GFAP) and rhodopsin (RHO). RESULTS: Delayed treatment of MSCs effectively alleviated the severity of intraocular inflammation with relative intact of outer retinal structure and function. Moreover, double therapies with longer interval led to an even better clinical evaluation, as well as a trend of decrease in relapse and amelioration of retinal function. MSC therapies also effectively reduced GFAP expression and increased RHO expression in the retina. CONCLUSION: MSC administration can effectively treat developed diseases of rEAU, and multiple therapies can provide additional therapeutic benefits.