Non-alcoholic fatty liver disease (NAFLD) is becoming ever more common in children, due to the increasing global prevalence of obesity. The first-line treatment consists of weight loss through a combination of a healthy diet and exercise. The objective of this study was to determine the effects of a Mediterranean Diet or a low-fat diet on reducing hepatic steatosis and insulin resistance in children with NAFLD. This 12-week randomised clinical trial was conducted with children aged 9-17 years diagnosed with NAFLD and randomised into either a Mediterranean Diet or a low-fat diet group. By the end of the study, hepatic steatosis had decreased significantly in both groups (p < 0.001). Liver enzymes also improved significantly, while significant decreases were observed in insulin resistance in both groups, although this decrease was greater in the Mediterranean Diet group (p = 0.010). This study demonstrated that a decrease in hepatic steatosis and an improvement in insulin sensitivity can be achieved with both a Mediterranean Diet and a low-fat diet over 12 weeks, with no significant decrease in the energy required for growth, in children with NAFLD.