Thyroid dysfunction is frequently associated with functional disturbances of the brain. We performed a meta-analysis of previous positron emission tomography and single-photon emission computed tomography studies using a coordinate-based technique of activation-likelihood estimation (ALE) to investigate the potential background of neuropsychiatric complications in patients with hypo- and hyperthyroidism. We performed a systematic search of MEDLINE and EMBASE for English-language publications using the keywords of "positron emission tomography", "single-photon emission computed tomography", and "thyroid". The software GingerALE ver 2.3.6 was used to transform all reported coordinates into stereotactic Montreal Neurological Institute space. A threshold of uncorrected p < 0.001 (minimum volume of 200 mm3) was applied to the resulting ALE map using cerebral metabolic rate of glucose (CMRglu), and cerebral blood flow (CBF). Six studies were eligible for inclusion in the study; 4 studies of cerebral metabolic rate of CMRglu, and 2 studies of CBF. In hypothyroidism, significant decreases in CMRglu were identified in 3 clusters including left anterior cingulate, right inferior occipital gyrus, and right cuneus. In hyperthyroidism, a significant decrease in CMRglu was identified in right superior frontal gyrus. In hypothyroidism, a significant decrease in CBF was observed in left postcentral gyrus. In conclusion, several brain regions showed altered CMRglu and CBF in patients with thyroid dysfunction compared with euthyroid controls. These findings might account for underlying mechanisms of thyroid hormones on psychological and physiological effects on brain.