The aim of this study was to investigate the potential of Flaxseed oil and fennel essential oil to improve insulin resistance due to PCOS in rats as a small mammal model which can be generalized to larger mammals. In an assay, 30 adult female Wistar rats (Age = 5to6 month and BW = 267 ± 20 g) were used in a completely randomized design with 5 experimental groups which it has 6 rats in each group. Experimental groups were: 1) control rats fed ordinary diet (CON group), 2) PCOS rats fed ordinary diet (PCO group), 3) PCOS rats fed ordinary diet + fennel essential oil + falxseed oil (PCO+Fennel+Flaxseed group), 4) PCOS rats fed ordinary diet + fennel essential oil (PCO+Fennel group) and 5) PCOS rats fed ordinary diet + flaxseed oil (PCO+Flaxseed group). Rats were injected with a single dose of estradiol valerate (4 mg estradiol valerate + 0.2 ml antiseptic sesame oil/kg BW) to induce poly cystic ovaries. The fennel essential oil (100 mg/kg BW/day) and flaxseed oil (429 mg/kg BW/day) were orally gavaged in a 50 days period. The results of this study show that body mass index and the amount of ovarian cysts were affected by treatments (p 0.05) and comparing control group were higher for PCOS rats fed flaxseed oil and (or) fennel essential oil. Feeding flaxseed oil and (or) fennel essential oil increased normal follicles. Also, Feeding flaxseed oil and (or) fennel essential oil decreased right ovary weight (p 0.05) and Feeding flaxseed oil with fennel essential oil significantly decreased left and sum of both left and right ovaries weights. Feeding flaxseed oil decreased fasting blood glucose (p 0.05) and HOMA-IR index, but increased progesterone concentration, QUIKI index, HOMA-? index and insulin concentration. Feeding fennel essential oil increased progesterone concentration, insulin concentration, HOMA-? and QUIKI index and decreased testosterone concentration (p 0.05), fasting blood glucose concentration and HOMA-IR. Feeding flaxseed oil with fennel essential oil increased blood glucose level and HOMA-IR index (p 0.05), but decreased HOMA-? and QUIKI indexes. Pathologically, No sign of lesion and damage was found in rats liver fed flaxseed oil and (or) fennel essential oil. Under the PCOS condition, the amount of Langerhans islets decreased, in contrary, feeding flaxseed oil and (or) fennel essential oil improved this condition. Keywords: Poly Cystic Ovary Syndrome, Insulin Resistance, Flaxseed oil, Fennel essential oil, Blood metabolites, Histology