Rheum rhabarbarumhas been widely used as a herbal medicine and food in China. The objective of this study was to investigate the cytoprotective action and underlying mechanisms of rhein, one active ingredient isolated from R. rhabarbarum, on H2O2-challenged rat small intestine epithelial cells (IEC-6 cells). H2O2-challenged IEC-6 cells were incubated in the pretreatment with or without rhein or LY294002, a PI3K/Akt inhibitor. The cell viability, apoptosis, intracellular reactive oxygen species (ROS), and antioxidants were measured. The expressions of heme oxygenase 1 (HO-1), nuclear factor erythroid 2-related factor (Nrf2), Akt, and p-Akt were evaluated by western blotting. Meanwhile, LY294002 was also used to investigate the role of PI3K/Akt in the rhein-induced cytoprotective role. The results showed that pretreatment of rhein could reverse the inhibition of cell viability and suppress the apoptosis, caspase-3 activity, and intracellular ROS induced by H2O2. Rhein also supported SOD activity catalase activity, glutathione S-transferase activity, and glutathione content. Furthermore, rhein induced the protein expression of HO-1 together with its upstream mediator Nrf2 and activated the phosphorylation of Akt in IEC-6 cells. LY294002 inhibited increased cell viability, upregulated the lowered apoptotic rate, and enhanced the weakened ROS levels. Although the inhibition of PI3K/Akt did not inhibit the Nrf2 nuclear level under 4 μM rhein, LY294002 inhibited the Nrf2 nuclear level under 2 μM rhein and blocked HO-1 expression. These data demonstrated that rhein protected IEC-6 cells against oxidative damage partly via PI3K/Akt and Nrf2/HO-1 pathways.