Dietary approaches are essential to control obesity, but the effectiveness of changes in meal frequency (MF) as a strategy for body weight loss or maintenance remain unclear. This study aimed to evaluate the influence of MF of a hypocaloric diet on weight loss, body composition, active ghrelin levels and metabolic indicators of obese women. This is a randomized, parallel clinical trial, including 40 women divided into two groups that received a hypocaloric diet with different MFs: MF6: six meals per day, and MF3: three meals per day. Dietary, laboratory, anthropometric and body composition indicators were assessed, as well as energy expenditure (EE), before and after the 90 days of the intervention. Dietary consumption did not differ between groups, before or after intervention. The two groups reduced their energy intake after intervention, but there were no differences between the groups. Waist circumference (WC) was reduced and resting metabolic rate had increased in the MF3 group at the end compared to baseline. Moreover, there was a significant difference in the triglyceride levels between groups after intervention, with an important reduction in the MF3 group, although changes in body composition, blood glucose, plasma ghrelin levels and EE variables did not differ between the groups at the end. It is concluded that, the hypocaloric diet with different MF each day did not change weight loss, body composition or insulin responsiveness, but there was an improvement of triglyceridemia in the MF3 group. The present study suggests that eating snacks between meals is not an important factor for weight loss and improvement of metabolic health in women with obesity.