Background Neural cell adhesion molecule (NCAM) is a glycoprotein and plays an important role in cell-cell adhesion, neural migration, neurite outgrowth, synaptic plasticity and brain development. We investigated the relationship between the serum NCAM concentration and cognitive deficit in first episode drug naïve schizophrenia (FES) patients. Methods Thirty FES patients and thirty healthy controls were recruited for this study. Psychiatric symptoms were assessed by the positive and negative syndrome scale (PANSS). Cognitive functions were assessed by measurement and treatment research to improve cognition in schizophrenia (MATRICS) and consensus cognitive battery (MCCB). Serum levels of NCAM were determined by ELISA. Results Schizophrenia patients had decreased serum NCAM concentrations than controls (−30%, p <0.001). Cognitive scores were significantly lower in FES patients than healthy controls (−34%, p <0.001). The NCAM concentrations were positively correlated with the total scores of MCCB (r =0.438, p =0.003). Multiple regression analysis confirmed that serum NCAM concentration was an independent contributor to MCCB total Scores. Conclusions There were a close relationship between the serum NCAM concentrations and cognitive deficits in FES patients. Since NCAM has an important role in neurodevelopmental processes, these results support the neurodevelopmental dysfunction hypothesis of schizophrenia and suggest that an altered NCAM may be one of the risk factors for schizophrenia including cognitive deficits.