Foundation models hold promise for generalizable analysis of structural brain magnetic resonance imaging (MRI) scans across diverse populations and imaging conditions. However, existing models typically rely on centralized pretraining using data pooled across cohorts, which is constrained by privacy and data-governance requirements. Moreover, larger cohorts can dominate optimization, underutilizing anatomical information from smaller cohorts and limiting generalization. Here we present BrainFedFM, a structural brain MRI foundation model federatively pretrained on 164,707 three-dimensional scans drawn from diverse real-world data distributions and organized across 42 federated sites. BrainFedFM uses dual-priority federated pretraining, in which spatial-priority masking emphasizes informative anatomical regions during local training, while site-priority aggregation adaptively weights contributions during global aggregation. Across 20 downstream datasets spanning 17 classification, regression and segmentation tasks, BrainFedFM achieved the state-of-the-art performance across seven foundation models, including four centralized models, while showing consistent advantages in classification and regression tasks and strong robustness under underrepresented populations and challenging imaging conditions. These findings demonstrate the generalizability of BrainFedFM and highlight federated pretraining as a practical strategy for developing neuroimaging foundation models from distributed data without pooling raw images.

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