Introduction: Transplantation of ovarian tissue is a fertility restoration technique in patients undergoing chemotherapy and radiotherapy. A major issue associated with ovarian transplantation is ischemia/reperfusion injury that leads to depletion and apoptosis of follicles. L-carnitine has antioxidant and anti-inflammation properties and can therefore be used to improve follicular survival and ovarian structure following transplantation. Methods: Naval Medical Research Institute (NMRI) mice (at the age of 4–5 weeks) were divided into 3 groups: control, autograft and autograft + L-carnitine (200mg/kg daily intraperitoneal injections). Seven days after ovary autografting, the serum levels of malondialdehyde (MDA), total antioxidant capacity, tumor necrosis factor alpha (TNF-α), interleukin (IL)-6 and IL-10 were measured. Ovary histology, serum concentrations of progesterone and estradiol were also measured 28 days after autotransplantation. Data were analyzed using one-way analysis of variance (ANOVA) and Tukey's test, and the means were considered significantly different at P<0.05. Results: In the autografted + L-carnitine group, the total volume of the ovary, the volume of the cortex, the number of follicles, the serum concentrations of IL-10, estradiol and progesterone significantly increased compared to the autografted group. In the autografted + L-carnitine group, serum concentrations of IL-6, TNF-α and MDA were significantly decreased compared to the autografted group. Conclusion: Our results indicated that L-carnitine can ameliorate the consequences of ischemia-reperfusion on the mice ovarian tissue following autotransplantation.