Hypothyroidism remains a pressing concern. Laser irradiation is a widely used treatment option for patients with thyroid pathologies. Its efficacy depends on the applied dose. Changes in the form and volume of the structural components of the glands, such as thyrocytes and follicles, are dose-dependent and signal their functional state, which affects production, accumulation and secretion of thyroid hormones. The aim of our study was to explore the effect of infrared medium-power laser with total energy densities of 112 J/cm² and 450 J/cm² on the morphology and function of the thyroid and its follicles in health and hypothyroidism. The experiment was conducted in male rats. It was demonstrated that laser radiation affects the morphological state of thyrocytes and follicles of both intact animals and animals with experimentally induced hypothyroidism. Comparison of two laser regimens revealed that 112 J/cm² energies stimulated tissue regeneration and thyroid activity in general, whereas 450 J/cm² energies suppressed those processes. Our findings can be used to study hypothyroidism treatment options in the experimental setting.