Background: Immunological checkpoints inhibitor (ICI) Pembrolizumab (PEMB) is a monoclonal antibody that induces a potent antitumor immune response. Hypothyroidism and adrenal insufficiency have been associated with its addition to the therapy protocol. Conditioned media (CM) is a culture media for stem cells comprising soluble proteins, lipids, nucleic acids, and extracellular vesicles (EV). Aim of the Work: This research aimed to determine whether mesenchymal stem cells conditioned media (MSCs-CM) could ameliorate thyroid gland histological disruptions caused by pembrolizumab. Materials and Methods: 45 adult male rats were incorporated in this work and classified into: control group (I), Pembrolizumab treated group (II): Pembrolizumab was administered intraperitoneally (i.p.) at a dose of 3 mg/kg three times a week for four weeks, and conditioned media treated group (III): was treated as group II and then received 200μl of MSCs-CM via tail vein twice a week for three weeks. We measured thyroid hormones and oxidative markers. The thyroid gland was examined by light and electron microscopy. Statistics were used to analyze all the data. Results: PEMB group shows desquamation of follicular cells into the lumen, cytoplasmic vacuolations and wide interstitial spaces among follicles. Some follicles appear involuted, others appear dilated and some follicles lack colloid. MSCs-CM group shows improvement in the thyroid sections' structural appearance. The majority of the follicles are colloid-filled. Cuboidal cells having large, rounded central nuclei lined the majority of thyroid follicles. Some follicles still have vacuolated cytoplasm. Conclusions: MSCs-CM is found to play a therapeutic role to improve PEMB thyroid ultrastructure histological alterations.