Exposure to laser radiation is an interesting method of treating hypothyroidism and autoimmune thyroiditis. Its effect depends on the applied radiation dose. Degranulation of stromal mast cells of the thyroid gland (mastocytes) is dose dependent; release of granular contents into the surrounding tissues may affect microcirculation, result in the increased activity of the thyroid epithelium or stimulate the thyroid. Our study aimed to investigate the effect of moderate-intensity infrared laser radiation at total surface doses of 112 and 450 J/cm on the functional state of mast cells and blood serum levels of thyroid gland hormones in healthy and hypothyroid subjects. The experiment was carried out in 78 random-bred mature male rats. Hypothyroidism was modeled by per os administration of 25 mg/kg Mercazolil (Akrikhin, Russia) for 21 days. Radiation therapy was performed using a IRE-Polus laser with a wavelength of 970 nm (NTO IRE-Polus, Russia). The animals received radiation therapy for 5 days and were sacrificed 1, 7, and 30 days after the experiment. Subsequently, we calculated the total number of mast cells, degranulated mastocytes, mastocytes with degree 1, 2 and 3 degranulation, degranulation coefficient, and levels of TSH in blood serum. Mast cells of the intact thyroid gland demonstrated low sensitivity to laser radiation, but hormone levels changed soon after radiation was discontinued. In the animals with hypothyroidism induced by thiamazole (the active component of Mercazolil), activation of mast cells was observed in the recovery period after the drug was discontinued. Hypothyroidism was accompanied by changes in TSH, T and T levels in blood serum. Comparison of the effects of two laser therapy modes in the animals with induced hypothyroidism revealed increased functional activity of mastocytes and normalized levels of secreted hormones at a total dose of 112 J/cm and reduced mast cell activity at a total dose of 450 J/cm.