Fatigue is one of the most common side effects of dialysis in hemodialysis patients and is associated with several psychological and physical complications. A new low-risk treatment for these patients is the use of complementary and alternative medicine such as aromatherapy. This study aimed at comparing the effects of inhaling lavender and orange extracts in hemodialysis patients. This randomized clinical trial (crossover) was conducted on 30 hemodialysis patients who were referred to hemodialysis center of Imam Khomeini Hospital in Zabol during February 2015-April 2016. Patients were divided into two groups of 15, each of which separately received orange and lavender aromatherapy. Data were collected using a demographic questionnaire and the Multi-dimensional Fatigue Inventory (MFI-20). The demographic questionnaire included age, sex, marital status, occupation, education, and duration of dialysis. Descriptive statistics and paired t-test were used for data analysis. Paired t-test showed a significant relationship between fatigue levels and inhalation of orange extract at the end of the first week (P=0.002); however, no significant relationship was observed in the second week. No significant relationship was observed between fatigue levels and inhalation of lavender extract (P=0.662). Considering the effect of orange extract, orange aromatherapy can be used as an easy, safe, non-invasive and relatively inexpensive nursing care.