Background The metabolic syndrome (MetS) and cognitive impairments are common in schizophrenia. Both are associated with poor outcomes, which have received increasing medical and mental health attention. Whether MetS is associated with impaired cognitive functions in schizophrenia has not been thoroughly addressed. The aim of this study was to compare the association between patients with and without MetS and its contributing components with neurocognitive performance. We hypothesized that patients with MetS would be associated with more impaired cognitive performance. Methods 159 patients with schizophrenia or schizoaffective disorder, with available metabolic data were included in the study. Patients were classified as either having or not having MetS as defined by the NCEP Adult Panel-III criteria. All patients completed neurocognitive and metabolic tests. Results Of the 159 patients, 43.34% had MetS. Patients without the MetS performed significantly better on tests measuring processing speed (p=0.050), attention/vigilance (p=0.040), working memory (p=0.041) and problem solving/reasoning (p=0.050) compared with those with MetS. Patients with MetS showed significantly lower cognitive domain scores. After Bonferroni correction greater waist circumference was associated with lower scores on attention/vigilance (β=−0.551; p≤.0083), HDL was positively associated with scores on attention/vigilance (β=0.900, p≤.0083) and higher triglycerides were associated with lower scores on attention/vigilance (β=−1.004, p≤.0083). Conclusions Schizophrenia patients with MetS showed significant cognitive impairments in three key cognitive domains. Aggressive medical treatment of the constituent components of MetS may provide the potential for important beneficial effects on patients' cognitive functioning.