Aim and background: Thyroid hemiagenesis (THA) is a rare congenital condition where one lobe of the thyroid gland fails to develop. Most cases are asymptomatic and require no treatment. However, some cases may develop various morphological, functional, and neoplastic lesions. Case description: We report a case of a 30-year-male who presented with right neck swelling for 3 months, which moved on deglutition. He was clinically euthyroid. Ultrasound neck showed a well-defined TIRADS 3 nodule of ~5 × 3.7 × 2 cm in the right lobe of the thyroid with a significantly small left thyroid lobe. Fine needle aspiration cytology (FNAC) from the nodule was suggestive of papillary carcinoma of the thyroid (PTC) (BETHESDA 6). The patient was planned for total thyroidectomy with central compartment lymph node dissection (CCLND). Intraoperatively, an enlarged 5 × 6 cm right lobe of the thyroid was visualized attached to a small 1.5 × 1.5 cm lobe without its separate neurovascular supply. The final histopathology report was suggestive of a follicular variant of papillary thyroid carcinoma with no gross extrathyroidal extension and a Ki-67 index of 4–5%. The patient is currently on regular follow-up as per the follow-up protocol for PTC. Conclusion: Thyroid hemiagenesis with a follicular variant of papillary carcinoma in the remnant thyroid lobe is a rare entity with only one reported case in the indexed literature. It poses a diagnostic challenge as most cases are asymptomatic, along with challenging management, as there is no standardized protocol for its management, thus necessitating the need for further studies. Clinical significance: The case is a rarity, with only one similar reported case in the indexed literature. There is a higher incidence of the development of carcinoma in these patients but the evidence available is sparse. Due to majority of these cases being asymptomatic, it poses a diagnostic challenge and necessitates the need for development of a standardized protocol for its screening and management.