Objective To study the effect of magnetic stimulation on the expression of B cell lymphoma/leukemia gene 2 ( Bcl-2 ) and caspase-3 genes, and the apoptosis of neurons in rats with spinal cord injury (SCI).Methods Sixty rats were randomly divided into a magnetic stimulation group, a model group and a sham-operation group. An SCI model was established in the magnetic stimulation and model groups. The magnetic stimulation was applied at the 6th, 12th, 24th and 72nd hour after the operation to the rats in the magnetic stimulation group, and sham magnetic stimulation was given to the model group and sham-operation group rats at the same time points. Two hours after treatment, 5 rats of each group were sacrificed and their injured spinal cords were sectioned. The gene expressions were detected using immunohistochemical techniques, and apoptosis of neurons was observed by the TUNEL method. Results Few apoptotic cells were found in the sham-operation group, but more were found in the model group. Apoptotic cells in the magnetic stimulation group were significantly fewer than in the model group. The expression of both Bcl-2 and caspase-3 in the magnetic stimulation and model groups was significantly higher than in the sham-operation group at the different time points. Expression of Bcl-2 in the magnetic stimulation group was significantly higher than in the model group, but expression of caspase-3 in the magnetic stimulation group was significantly lower than in the model group. Conclusions Magnetic stimulation up-regulates the expression of Bcl-2 genes and down-regulates the expression of caspase-3 in injured neurons. Magnetic stimulation might have protective and rehabilitative effects after human SCI.