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The aim of this study was investigated the effects of fennel supplementation with energy-restricted diets on body fat and muscle percentage and insulin resistance in women with PCOS. Sixty-four overweight/obese women with PCOS were randomly allocated to 4 groups for 12 weeks as follows: (1) standard diet + fennel (SDF), (2) high-protein, low-carbohydrate diet supplemented with fennel (HPF), (3) standard diet + placebo (SDP), and (4) high-protein, low-carbohydrate diet + placebo (HPP). After 12 weeks of intervention, there were significant changes in the percentage of body fat and muscle in all groups. Decreasing in fasting insulin was −4.12 micIU/ml (P = 0.01) for HPF and −4.5 micIU/ml (P = 0.03) for SDP groups. In addition, HOMA-IR significantly decreased in HPF (P = 0.02) and SDP (P = 0.02) groups. Energy-restricted diets independent of dietary composition improved the body fat and muscle percentage and insulin resistance indices in women with PCOS. High-protein diet and fennel compared with standard diet and placebo had no significant effect on insulin resistance, body fat and muscle.