Objective The clozapine/N-desmethylclozapine (NDMC) ratio is proposed to be used as a predictor of cognitive performance in clozapine- treated patients, as its principal metabolite, NDMC, has an opposite action with clozapine on the cholinergic system. The aim of this study is to determine whether clozapine has influence on cognitive performance in accordance with changes in the clozapine/ NDMC in patients with schizophrenia. Methods The data of fifteen patients with schizophrenia, who had initial and follow-up assessments after starting clozapine treatment, were retrospectively collected. The assessments included clinical scale, cognitive battery, and pharmacological data including plasma concentrations of clozapine and NDMC. The data were analyzed with Pearson correlation and stepwise multiple regression analyses. Results ΔAttention/vigilance, Δsocial cognition, and Δcomposite score had a significant correlation with Δclozapine/NDMC ratio, while ΔWorking memory had correlation with Δclozapine concentration and ΔNDMC concentration, and Δsocial cognition had association with Δclozapine concentration. Multiple regression analysis showed that Δattention/vigilance had negative association with Δclozapine/NDMC ratio, Δworking memory had negative relation with Δclozapine concentration, and that Δsocial cognition had negative association with Δclozapine concentration. Conclusion This finding implicates that lowering the clozapine/NDMC ratio could enhance cognition in patients with schizophrenia treated with clozapine.