Anti-leucine-rich glioma-inactivated 1 (LGI1) encephalitis is a rare type of non-paraneoplastic limbic encephalitis (LE) mainly characterized by seizures, cognitive disorder, faciobrachial dystonic seizures (FBDS), hyponatremia, insomnia, and autonomic dysfunction. Here, we report the case of an elderly female patient who tested positive for antibodies against LGI1 and was initially thought to have Hashimoto encephalopathy (HE) due to its similar clinical features and the patient's high titers of antithyroid antibody. Interestingly, during the course of the disease, the patient exhibited typical FBDS and brain magnetic resonance imaging (MRI) showed a hyperintense signal evolution from T2/Fluid attenuated inversion recovery (FLAIR) to T1-weighted image in the bilateral basal ganglia (BG), which have rarely been reported previously.