Cognitive impairment is one of the core symptoms in schizophrenia, which reflects the neurodevelopmental deficits in the etiology of this disease. Brain-derived neurotrophic factor (BDNF) plays an important role in various neurodevelopmental processes. Growing evidence has shown that BDNF may be involved in the etiology of schizophrenia. The aim of this study was to examine the association of the BDNF Val66Met polymorphism with cognition in patients with schizophrenia. Various neuropsychological tests including the Wechsler Adult Intelligence Scale-Revised, the Wechsler Memory Scale-Revised, and the Wisconsin Card Sorting Test (WCST) were employed in a sample of 112 antipsychotic-naïve patients with schizophrenia and 63 healthy controls. We examined the Val66Met polymorphism in the 112 patients and 394 controls. Among the patients, cognition was compared between Met allele carriers and non-Met allele carriers. A wide range of cognitive deficits were demonstrated in the schizophrenic patients, compared with the controls (Ps < 0.01). No significant differences of genotype or allele distribution were identified between patients and controls. The patients with Met allele showed more percent WCST perseverative errors than those without Met allele (P = 0.007). After stratification based on gender, an association between the Met allele and a higher percentage of perseverative errors was found in male patients (P = 0.014), but not in females (P = 0.09). Cognitive performance is broadly impaired in schizophrenic patients. The BDNF Val66Met polymorphism may be involved in the impaired executive function. This effect may have gender-specific characteristics.