Ectopic intrathyroidal thymomas are an exceedingly rare clinical entity that can be challenging to diagnose. This report describes a 39-year-old Japanese woman who presented with prominent left-sided thyroid enlargement that was thought to be a dominant thyroid nodule by ultrasound. Two fine-needle aspiration biopsies showed an atypical lymphoid proliferation that was suspicious for although not diagnostic of a low-grade lymphoma. A diagnosis of ectopic intrathyroidal thymoma was made only after appropriate histopathologic assessment of the surgical specimen.