Spermatogenesis is regulated by a cascade of steroid regulated genes in the testis. Recent studies suggested that acupuncture may improve fertility in men with abnormal semen parameters. Yet, the underlying mechanisms in which acupuncture enhances spermatogenesis remain largely unknown. Here we used a scrotal heat-treated rat model to study the effect of electroacupuncture (EA) on recovery of spermatogenesis. In this model, spermatogenesis was disrupted by 30 min scrotal heat treatment at 43°C. Ten sessions of EA were given at Baihui (GV20), Guanyuan (CV4), Zusanli (ST36) and Sanyinjiao (SP6) from day 9 to day 36 post-treatment. Sperm motility and production, morphology of the germinal epithelium by Johnsen’s scoring, germ cell apoptosis by TUNEL staining, proliferation by proliferating cell nuclear antigen (PCNA) staining, as well as serum testosterone and inhibin B levels by immunoassays were evaluated on day 0, 1, 9, 25, 37, 46, 56 and 79. When compared with the heat-treated (H) group, the heat-treated plus EA (H+EA) group showed a significant increase (p < 0.05) in PCNA-positive cells and inhibin B levels on days 37 and 46, and a higher Johnsen’s score till day 56. On day 79, motile spermatozoa could be found in the vas deferens of H+EA group only. Consistently, there was a trend of improved motility and increased number of motile epididymal spermatozoa in the H+EA group than the H group; while apoptosis of germ cells and serum testosterone levels were similar between the two groups. Taken together, EA enhanced germ cell proliferation through improvement of Sertoli cell functions. This may facilitate the recovery of spermatogenesis and may restore normal semen parameters in subfertile patients.