Low triiodothyronine syndrome is a physiological adaptation encountered in anorexia nervosa (AN) and generally improves with sufficient weight gain. However, when a primary thyroid pathology accompanies AN, both the evaluation of thyroid hormone levels and the management of the co-morbid disease become more challenging. Hashimoto thyroiditis could complicate the management of AN by causing hyper- or hypothyroidism. AN could also negatively affect the treatment of Hashimoto thyroiditis by altering body weight and metabolic rate, as well as by causing drug non-compliance. We present the case of a 15-year-old boy with comorbid AN restrictive sub-type and Hashimoto thyroiditis. In this case report, we aimed to draw attention to the challenges that could be encountered in the diagnosis, treatment, and follow-up of patients with AN when accompanied by Hashimoto thyroiditis.