Obesity is associated with metabolic disorders which affect male and female fertility. Boswellia carterii is rich in phenolic compounds and well known by its antioxidant, anti-inflammatory, hypoglycemic and hypolipidemic effect. The aim of this study was to study the potency of boswellia, if administered for complete reproductive cycle, to correct the metabolic disruption and improve the reproductive performance of animals. Boswellia oil was extracted and fractionated to identify its phenolic content. Microcapsules were prepared from the resin water extract using Arabic gum and maltodextrine. Antimicrobial activity was done for water extract. Forty Sprague Dawely rats were classified into 4 groups. Animals were separated according to sex and fed on normal fat diet (NFD), NFD beside boswellia microcapsules (500 mg/kg body weight), high fat diet (HFD) and HFD beside boswellia microcapsules at the same dose respectively. The experiment lasted for 60 days. Animals were sacrificed. Fecal colony count was done, the collected plasma was analyzed, epididymal spermatozoa profile was done. Histopathological examination and immune histochemistry were done to genital organs. Feeding on HFD resulted in hyperlipidemia, hyperglycemia, and low level of steroid hormones, IGF, insulin, TSH and the antioxidant enzymes. Elevated levels of leptin, lipid profile, glucose, liver enzymes and oxidative markers were also demonstrated. HFD negatively affected male and female fertility confirmed by histopathological examination. The immune staining showed strong expression of both markers (Caspase-3 and iNOS). Daily administration of boswellia microcapsules corrected all the metabolic and pathological disorders and enhanced animal fertility.