Although the recipient site in burn wounds is dressed with universally accepted materials, the ideal management of split-thickness skin donor sites remains controversial. The aim of our study is to compare two methods of wound dressing in donor sites of split-thickness skin graft in patients undergoing burn wound reconstructive surgery. Forty-two consecutive patients with second- and third-degree burns with a total body surface area between 20 and 40 % were enrolled in this randomized clinical trial conducted in Motahari Burn Hospital in Tehran, Iran. In each patient, two anatomic areas with similar features were randomly selected as intervention and control donor sites. The intervention site was dressed with amniotic membrane, whereas the control site was treated with Vaseline-impregnated gauze. Wounds were examined daily by expert surgeons to measure the clinical outcomes including duration of healing, severity of pain, and infection rate. The mean ± SD age of patients was 31.17 ± 13.72 years; furthermore, burn percentage had a mean ± SD of 31.19 ± 10.56. The mean ± SD of patients' cooperation score was 1.6 ± 0.79 in the intervention group compared with 2.93 ± 0.71 in the control group, revealing a statistically significant difference (P < 0.05). Duration of wound healing was significantly shorter (P < 0.05) in the intervention group (17.61 ± 2.56 days) compared with the control group (21.16 ± 3.45 days). However, there was no significant difference in terms of wound infection rate between donor sites in the control and intervention groups (P > 0.05). Amniotic membrane as an alternative for dressing of skin graft donor sites provides significant benefits by increasing patients' comfort via diminishing the number of dressing changes and facilitating the process of wound healing.