Graph neural networks (GNNs) can exhibit unfair behavior even when sensitive attributes are excluded from node features, because graph topology and message passing propagate group-correlated signals under sensitive homophily. Existing fairness-aware GNN methods mainly constrain representations or prediction distributions at a global level, without explicitly controlling the local structural pathways through which biased information propagates during aggregation.

We propose Subgraph Filtering for Fair Graph Neural Networks (SF-GNN), a lightweight and architecture-agnostic framework that mitigates structural bias at its source. SF-GNN identifies bias-prone edges by combining sensitive homophily with structural propagation amplifiers, including hub participation and triadic closure.

It then incorporates stochastic edge filtering into each message-passing step to selectively downweight or remove these edges while preserving the remaining graph structure. Training further incorporates a statistical-parity regularizer with a warm-up schedule to stabilize optimization.

Experiments on five benchmark datasets show that SF-GNN achieves consistent fairness improvements while maintaining competitive predictive performance, leading to a better fairness--accuracy trade-off than recent fairness-aware GNN baselines.