Introduction: Squamous cell carcinoma (SCC) is a rare malignancy of invasive epithelium with keratinocyte differentiation, and it is the most common form of eyelid malignant neoplasm, comprising 5-10% of malignancies. While SCC rarely affects the orbit, it may be involved through local invasion from a cutaneous primary site or extension by perineural invasion. Only 11 cases of primary orbital SCC have been reported until now. Here, we present a case of primary carcinoma of the right orbit with coexisting Carney’s syndrome, a rare genetic disorder associated with multiple endocrine neoplasias (MEN) syndromes. Case: A 62-year-old south Asian male presented with a painful swelling in the lateral aspect of the right eyebrow and protrusion of the eyeball in August 2020. He had a history of excision of Right atrial Myxoma in March 2020. Orbital computerized Tomography (CT) and Positron Emission Tomography (PET-CT) scans revealed an enhancing soft tissue lesion in the right orbit with involvement of frontal and ethmoid sinuses. Biopsy confirmed HPV related poorly differentiated squamous cell carcinoma, positive for HPV-related markers. The patient received concurrent chemo irradiation with Cisplatin. Follow-up done PET-CT done 3 months later showed a new lesion appeared in the right orbital region and right lobe of thyroid. Later had surgical excision and total thyroidectomy and Histopathological examination (HPE) from orbit was reported as invasive SCC and from the thyroid was reported as synchronous papillary thyroid cancer. The patient’s proptosis resolved, and subsequent PET-CT and Magnetic Resonance Imaging (MRI) scans did not show any residual or recurrent disease. Conclusion: Primary SCC of the orbit is an extremely rare disease, and this case report presents the 12th reported case and the first one associated with Carney’s syndrome. As there is no standard treatment regimen for primary SCC of the orbit, this case highlights the use of multimodality treatment, including surgical excision and chemo irradiation. The findings emphasize the importance of early detection and management of this uncommon and life-threatening condition, providing hope for patients and aiding in the prevention of recurrence.