Coconut oil appears to help in weight loss and improve metabolic parameters associated with obesity. We evaluate the influence of coconut oil on the body composition, lipid profile and glycemia in men with obesity. A controlled, randomized clinical trial was performed with 29 adult men affected by obesity. They were randomized between two groups receiving a daily intake of 1 tablespoon (12 mL) of extra virgin coconut oil (CO, n = 15) or soybean oil (SO, n = 14), and an isoenergetic balanced diet. The anthropometric profile, lipid profile and glycaemia were evaluated at the baseline and 45 days after intervention. The Mann-Whitney test was performed to compare the groups, and the Wilcoxon test was performed to compare the times. We considered a value of p < 0.05 as significant. There was no difference in anthropometric variables between the groups before and after intervention. The level of HDL cholesterol increased (3.67 ± 8.08 versus-3.79 ± 10.98, p = 0.02) and the TC/HDL cholesterol ratio decreased (-0.63 ± 0.82 versus 0.23 ± 0.80, p = 0.03) in the CO group, compared to the SO group. Coconut oil included in the isoenergetic balanced diet could increase HDL cholesterol and decrease the TC/HDL cholesterol ratio in men with obesity.