This study reports a framework to discriminate patients with schizophrenia and normal healthy control subjects, based on magnetic resonance imaging (MRI) of the brain. Resting-state functional MRI data from a total of 144 subjects (72 patients with schizophrenia and 72 healthy controls) was obtained from a publicly available dataset using a three-dimensional convolution neural network 3D-CNN based deep learning classification framework and ICA based features. We achieved 98.09 ± 1.01% ten-fold cross-validated classification accuracy with a p-value < 0.001 and an area under the curve (AUC) of 0.9982 ± 0.015. In addition, differences in functional connectivity between the two groups were statistically analyzed across multiple resting-state networks. The disconnection between the visual and frontal network was prominent in patients, while they showed higher connectivity between the default mode network and other task-positive/ cerebellar networks. These ICA functional network maps served as highly discriminative three-dimensional imaging features for the discrimination of schizophrenia in this study. Due to the very high AUC, this research with more validation on the cross diagnosis and publicly available dataset, may be translated in future as an adjunct tool to assist clinicians in the initial screening of schizophrenia.