Methamphetamine (MA) abuse is related to risks to the cardiovascular system. The present study aimed to compare the effects of moderate-intensity aerobic training (MIAT) and vitamin E (Vit.E) supplementation on markers of cardiac apoptosis following MA exposure. Fifty-four rats were randomly divided into six groups. CON group did not receive MA, while the others received MA alone or in combination with MIAT, Vit. E, MIAT+Vit E, or paraffin (PAR). These groups received MA incrementally for 23 consecutive days. Vit.E and MIAT+Vit.E groups received vitamin E three times a week for six weeks. MIAT and MIAT+Vit.E groups exercised for 25-40 min. Immunohistochemical and gene expression analyses were performed on the heart tissues. Bax and TGF-β expression was significantly higher, while Bcl-2 and VEGF expression was significantly lower in the MA and PAR groups than in the other groups (p < 0.05). Bcl-2 and VEGF expression was higher, and Bax and TGF-β expression was significantly lower in the MIAT and MIAT+Vit.E groups than in the other groups (p < 0.05). In Vit.E treated groups, Bax and TGF-β expression were lower, and VEGF was higher than that in the MA and PAR groups, but higher than those in the CON, MIAT and MIAT+Vit.E groups. MA increased the expression of Bax and TGF-β, and decreased the expression of Bcl-2 and VEGF, suggesting increased cardiac apoptosis. In contrast, MIAT and Vit.E decreased the expression of Bax and TGF-β, suggesting a reduction in cardiac apoptosis induced by MA.