A revolutionary field that has the potential to change many facets of biology and medicine, including animal reproductive health, is nanotechnology. The biocompatibility of different nanoparticles has made them an effective drug carrier. Apart from this, they also increase the effectiveness and selectivity of treatments for diseases that affect the reproductive system. In case of females, the infertility is one of the major issues and the nanotechnology mediated IVF techniques incorporating polyethylene glycol (PEG) and hyaluronidase as nanomaterials has been used quite effectively. In the treatment of endometriosis, the application of cerium oxide nanoparticles and Poly (lactic-co-glycolic acid) (PLGA) have been seen to modulate the activity of endometrial gland by increasing the effectiveness of drugs in use. A viral-mediated gene transfer with nanotechnology has also been developed as a highly effective and non-invasive therapeutic option for the management of uterine fibroids. In case of ovarian cancer, the use of gold nanospheres, carbon nanotubes, polymeric nanoparticles and many others, has shown considerable promise for diagnosis and treatment. In case of males, innovative nanomedicines for benign prostatic hyperplasia have been made using PLGA and gold nanoparticles. The male infertility issues have also been addressed via nanotechnology like testicular abnormalities associated with malathion has been alleviated by the application of cerium dioxide nanoparticles. Nano-biosensor composed of zirconium metalorganic frameworks and gold nanoparticles are being used to examine the protamines (a biomarker for male infertility) in semen samples. The present chapter highlights all these applications of nanotechnology in treating various male and female reproductive disorders.