Allergen immunotherapy (AIT), or specific immunotherapy (SIT), is an effective treatment for inducing immune tolerance to specific allergens. It is widely used for allergic rhinitis, conjunctivitis, asthma, and Hymenoptera venom allergies, with recent applications to food allergies and atopic dermatitis. Despite its benefits, the use of SIT in patients with autoimmune diseases is controversial due to concerns about its potential to induce or exacerbate autoimmune conditions. This report examines a case of autoimmune hypothyroidism developing during AIT and the management decisions involved. A 26-year-old female with a history of moderate to severe persistent allergic rhinitis and childhood asthma presented with severe malaise, weakness, and fatigue over the past three months. She had a family history of asthma and allergic rhinitis. The patient had been on AIT for six months and was using intranasal fluticasone furoate nasal spray daily. Initial laboratory investigations prior to AIT showed normal thyroid function. Three months into AIT, she developed hypothyroidism, confirmed by elevated TSH levels and positive anti-TPO antibodies. A causality assessment suggested a "possible" link between AIT and hypothyroidism. However, a risk-benefit analysis favored the continuation of AIT along with the initiation of L-thyroxine therapy. After six months of thyroid hormone replacement, her TSH levels normalized, and her allergic rhinitis symptoms significantly improved. This case underscores the complexity of managing coexisting allergic and autoimmune conditions. The decision to continue AIT, despite the onset of hypothyroidism, was based on a thorough risk-benefit analysis, emphasizing the need for personalized treatment plans. Understanding the immunological mechanisms, particularly the balance between Th17 and Treg cells, is crucial. Neutrophils play a significant role as both effectors and modulators of immune responses. The clinical pharmacologist's recommendation was informed by these factors and the manageable nature of hypothyroidism with hormone replacement therapy. The continuation of AIT was justified by its benefits in managing allergic rhinitis and the manageable nature of hypothyroidism with hormone therapy. This case highlights the importance of personalized medicine and continuous monitoring in treatment decisions for patients with coexisting conditions.