Nanoemulsions (NEs), lipid nanocarriers, are emerging drug delivery systems that can carry drugs, increase bioavailability, and control their release. Although the pharmacological properties of NEs are widely studied, knowledge about their toxicity is scarce. Thus, the study aims to evaluate the possible toxic effects of two oral doses (250 & 500 mg/kg) of thymol nanoemulsion (T-NE) on the reproductive organs of male and female rats. The study included six animal groups; two male and female control groups, two male and female groups consumed T-NE low dose, and the last consumed T-NE high dose. Some biological parameters, sperm characteristics, biochemical parameters, and DNA fragmentation were measured along with histological examination. The results revealed the potential sensitivity of female reproductive organs to T-NE either at low or high doses. While male reproductive systems are only affected at the high dose significantly. A significant alteration was found in feed intake, body weight, relative organs weight, sperm count, and motility. Also, there was a marked elevation in the pro-oxidants malondialdehyde (MDA) and protein carbonyl products (PCs) along with a reduction in superoxide dismutase (SOD) are found. Besides toxic effects are found as altered ATP production, elevated DNA fragmentation, and altered reproductive hormonal balance. Microscopic features of the testis and ovaries are significantly affected by T-NE oral intake. In conclusion, the tested doses of T-NE showed a marked toxic effect on the reproductive organs of rats especially female rats. Which can shed light on testing the safety of consuming T-NE.