Lithium carbonate (LC) is known to alter thyroid gland function. Pomegranate (PG) is a fruit with multiple antioxidant and antiapoptotic properties. Here, we studied the effect of PG on LC-induced morphological and functional alterations in the thyroid glands of rats. Rats were divided into four groups: control, lithium, lithium-PG, and PG. After 8 weeks, the rats were sacrificed, the levels of thyroid hormones and oxidative stress markers were estimated, and thyroid tissues were subjected to histological, immunohistochemical, and ultrastructural evaluations. Compared to the control group, the lithium group showed significant changes in thyroid hormone levels, greater expression of the oxidant marker malondialdehyde, and lower expression of the antioxidant marker superoxide dismutase (SOD). Most of these changes improved upon PG treatment. Histological evaluation of the thyroid in the lithium group showed disorganization and follicle involution. Additionally, the periodic acid Schiff staining intensity and SOD immunoreactivity declined significantly, whereas the collagen fiber content and Bax immunoreactivity increased. The follicular ultrastructure showed marked distortion. These changes were mitigated upon PG treatment. In conclusion, PG alleviated the morphological and functional changes in the thyroid glands induced by LC by modulating apoptosis and oxidative stress.