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Abstract Background Support vector machines (SVMs) based on brain-wise functional connectivity (FC) have been widely adopted for single-subject prediction of patients with schizophrenia, but most of them had small sample size. This study aimed to evaluate the performance of SVMs based on a large single-site dataset and investigate the effects of demographic homogeneity and training sample size on classification accuracy. Methods The resting functional Magnetic Resonance Imaging (fMRI) dataset comprised 220 patients with schizophrenia and 220 healthy controls. Brain-wise FCs was calculated for each participant and linear SVMs were developed for automatic classification of patients and controls. First, we evaluated the SVMs based on all participants and homogeneous subsamples of men, women, younger (18–30 years), and older (31–50 years) participants by 10-fold nested cross-validation. Then, we hold out a fixed test set of 40 participants (20 patients and 20 controls) and evaluated the SVMs based on incremental training sample sizes (N = 40, 80, …, 400). Results We found that the SVMs based on all participants had accuracy of 85.05%. The SVMs based on male, female, young, and older participants yielded accuracy of 84.66, 81.56, 80.50, and 86.13%, respectively. Although the SVMs based on older subsamples had better performance than those based on all participants, they generalized poorly to younger participants (77.24%). For incremental training sizes, the classification accuracy increased stepwise from 72.6 to 83.3%, with >80% accuracy achieved with sample size >240. Conclusions The findings indicate that SVMs based on a large dataset yield high classification accuracy and establish models using a large sample size with heterogeneous properties are recommended for single subject prediction of schizophrenia.