Introduction Spermatogenesis is highly dependent on energy metabolism and spermatogenesis is very sensitive to compounds that interfere with mitochondrial energy metabolism and cellular respiration control. The purpose of this research was to investigate the role of exercise activity along with stem cells on the expression of some effective genes in mitochondrial biogenesis in azoospermic rats with busulfan. Methods In this experimental study, 30 8-week-old rats were selected and randomly divided into 6 groups after induction of the azoospermia model. Healthy, sham, azoospermia, azoospermia+exercise, azoospermia+cell group, and azoospermia+cell+exercise group were divided. One month after the creation of the model, one million stem cells were transplanted once into the vas deferens of each mouse. Swimming training was done daily for 30 minutes a day and 5 days a week for 8 weeks. Genes were measured by Real time-PCR method. One-way analysis of variance was used to analyze the data. All calculations were done using SPSS/23 statistical software and at a significant level of P≤, 0. 05. Findings The results showed that the induction of the azoospermia model caused a decrease in the expression of SIRT1 and AMPK genes in testicular tissue, and that exercise combined with cell therapy increased the expression of SIRT1 and AMPK genes in testicular tissue in azoospermic model rats. Conclusion In general, the results of the current research indicate that regular aerobic exercise such as low-intensity swimming helps in controlling the effects of infertility diseases through the maintenance and development of mitochondrial biogenesis in improving the spermatogenesis process.