This study aimed to investigate the correlation between endocannabinoids and polycystic ovary syndrome (PCOS), and the expression levels of endocannabinoids in different phases of menstruation. The expression of cannabinoid receptors (CB1) and fatty acid amide hydrolase (FAAH) in the endometrium were immunohistochemically stained and compared between women with PCOS and the control group. Integrated optical density (IOD) was assessed to analyze their expression levels. The CB1 and FAAH were expressed in endometrial epithelial cytoplasm. No significant difference in CB1 level was observed between PCOS and non-PCOS women. Additionally, the expression of CB1 did not fluctuate with menstrual cycle. However, the FAAH levels were lower in the PCOS group than the non-PCOS group (p < 0.05). FAAH levels in secretory phases were significantly elevated compared to menstrual and proliferative phases (p < 0.05). Our results demonstrate that the endocannabinoid system may play an important role in menstruation, and dysregulation of the system may result in PCOS.