The current research aimed to evaluate the effects of L-thyroxine-induced hyperthyroidism and melatonin administration on the histopathology of the thyroid and thymus glands and Bax immunoreactivity. The rats were divided into four groups, comprising ten rats each. Rats were given the following treatments for four weeks: Group I served as the control group; Group II received melatonin; Group III received L-thyroxine; and Group IV received both L-thyroxine and melatonin. The serum levels of total T3 (tT3) and total T4 (tT4) were assessed, as well as histological examinations of the thyroid and thymus and analysis of Bax immunoexpression in both organs. The obtained results showed that in rats with hyperthyroidism, melatonin administration caused a noticeably lower level of thyroid hormones. According to the histopathological examination, hyperthyroidism induced various deteriorating changes in the thyroid and thymus glands, while melatonin therapy reduced these adverse effects. The immunohistochemical analysis demonstrated that hyperthyroid rats displayed a substantial elevation in Bax expression in the thyroid and thymus glands. However, melatonin treatment in hyperthyroid rats resulted in a marked reduction in Bax expression. Thus, it could be concluded that hyperthyroidism induced a range of degenerative changes and markedly elevated Bax expression in thyroid and thymus tissues. However, melatonin intervention ameliorated these negative effects.