Long-chain n-3 fatty acids have been shown to regulate lipid metabolism and reduce fat accumulation in the liver. This trial investigated the effect of flaxseed oil, as a rich source of α-linolenic acid, on fatty liver and cardiometabolic risk factors in patients with non-alcoholic fatty liver disease (NAFLD). The randomised, double-blind, controlled trial was performed on sixty-eight NAFLD patients who were divided into flaxseed (n 34) and sunflower (n 34) oil groups. Patients were given a hypoenergetic diet (−2092 kJ/d) and 20 g/d of the corresponding oil for 12 weeks. Fatty liver grade, liver enzymes and cardiometabolic parameters were determined. The intention-to-treat approach was used for data analysis. Fatty liver grade significantly decreased in both groups (−0·68 in flaxseed v. −0·29 in sunflower, P = 0·002). Alanine aminotransferase and aspartate aminotransferase decreased in both groups (P < 0·01). Also, significant reduction was observed in blood glucose (P = 0·005) and fat mass (P = 0·01) in the flaxseed and muscle mass (P = 0·01) in the sunflower group. However, none of these alterations was significantly different between the groups. Weight, waist circumference and blood pressure were significantly decreased in both groups but only weight change was significantly different between the groups (P = 0·01). IL-6 did not significantly change in either group but showed a significant between-group difference (P = 0·03). Overall, the results showed that in the context of a low-energy diet and moderate physical activity, flaxseed oil may benefit NAFLD patients to improve fatty liver grade, weight and IL-6 compared with sunflower oil.