Secoemestrin C is an epitetrathiodioxopiperazine isolated from Aspergillus nidulans, which has only been reported in terms of inhibiting tumor cell proliferation. Here, we determined the immunomodulatory and hepatoprotective effects of secoemestrin C in a mouse model of acute autoimmune hepatitis. In an in vitro assay, purified hepatic mononuclear cells (MNCs) from C57BL/6J mice were stimulated with concanavalin A (Con A) in the presence of secoemestrin C, and cell proliferation and cytokine production were measured. In an in vivo assay, mice with or without secoemestrin C pretreatment were injected with Con A to induce acute hepatitis. The secoemestrin C treatment dose-dependently suppressed cell proliferation and proinflammatory cytokine secretion in Con A-stimulated hepatic MNCs in vitro. In Con A-challenged mice, pre-injection with secoemestrin C significantly decreased the generation of proinflammatory cytokines and ameliorated liver injury. Furthermore, pretreatment with secoemestrin C significantly inhibited the Con A-induced activation of NKT and conventional T cells, and decreased IFN-gamma production by these two cell populations. We conclude that secoemestrin C has an immunosuppressive effect on NKT and conventional T cells and has hepatoprotective activity in mouse autoimmune hepatitis. These findings provide new insights into the use of fungus-derived natural products for the treatment of autoimmune diseases.