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Resting‐state functional magnetic resonance imaging (rs‐fMRI) helps characterize regional interactions that occur in the human brain at a resting state. Existing research often attempts to explore fMRI biomarkers that best predict brain disease progression using machine/deep learning techniques. Previous fMRI studies have shown that learning‐based methods usually require a large amount of labeled training data, limiting their utility in clinical practice where annotating data is often time‐consuming and labor‐intensive. To this end, we propose an unsupervised contrastive graph learning (UCGL) framework for fMRI‐based brain disease analysis, in which a pretext model is designed to generate informative fMRI representations using unlabeled training data, followed by model fine‐tuning to perform downstream disease identification tasks. Specifically, in the pretext model, we first design a bi‐level fMRI …