There is increasing proof that polycystic ovary syndrome (PCOS) is associated with the increased frequency of thyroid disturbances. Chamomile (Matricaria chamomilla L.) herb and metformin showed therapeutic efficacy against polycystic ovary syndrome (PCOS). This study aimed to investigate the possible therapeutic effect of both chamomile flower extract and metformin against thyroid damage associated with PCOS in rats. The PCOS model was developed in rats by injecting estradiol valerate, and it was confirmed to be associated with thyroid hypofunction biochemically and pathologically. Treatment of PCOS rats with both chamomile extract and metformin resulted in an improvement in serum level of thyroid hormones (TSH, p < 0.01; T3 and T4, p < 0.05) and the disappearance of most thyroid gland pathological changes demonstrated by light and electron microscopes. They also reduced the level of serum estrogen (p < 0.01). Both chamomile extract and metformin decreased MDA (p < 0.05) and increased GPx and CAT (p < 0.01). Only chamomile extract increased GSH (p < 0.01). Both treatments reduced the apoptotic death of thyroid cells as noted by the reduction of caspase-3 immunoexpression (p < 0.01). In conclusion, both Matricaria chamomilla extract and metformin ameliorated hypothyroidism associated with PCOS through an antioxidant and antiapoptotic mechanism.