Mycophenolate mofetil (MMF) is an immunosuppressive agent widely applied in various autoimmune diseases, including autoimmune uveitis, a sight-threatening autoimmune disease mainly affecting the eyes. However, the mechanisms of action are not comprehensively understood. To investigate the potential impact of MMF on uveitis, we generated single-cell RNA sequence data from normal, experimental autoimmune uveitis (EAU) and MMF-treated EAU mice. We observed that some EAU-induced transcriptional changes were reversed by MMF treatment. Transcriptional data indicated that MMF may have a general inhibitory effect on the activation of immune cells during EAU. Each immune cell type showed a different response to MMF treatment. Pseudotime analysis showed that MMF treatment partly reversed the increased differentiation tendency from naïve to effector phenotypes of T and B cells in EAU. The reduced proportion of T-helper (Th)1 and T-helper (Th)17 cells after MMF treatment was confirmed using flow cytometry. MMF treatment downregulated the EAU-associated upregulation of several molecules (such as Cebpd, Pim1, Furin, Bhlhe40, and Hif1a) that promote pathogenic cytokine production by T helper (Th)-1 and Th17 cells. Abnormally enhanced immunoglobulin production, antigen processing, and presentation ability of B cells may also be inhibited by MMF treatment. In addition to T and B cells, MMF treatment countered EAU-induced transcriptional changes in other immune cells to different degrees. Overall, our findings provide novel insights into the mechanisms underlying MMF treatment and indicate that the therapeutic effect of MMF is not driven by a single molecule.