diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4ecc97adb613..8ac45e0b0de5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Fixed
 
+- Fixed `GraphMaskExplainer` for GNNs with more than two layers ([#8401](https://github.com/pyg-team/pytorch_geometric/pull/8401))
 - Breaking Change: Properly initialize modules in `GATConv` depending on whether the input is bipartite or non-bipartite ([#8397](https://github.com/pyg-team/pytorch_geometric/pull/8397))
 - Fixed `input_id` computation in `NeighborLoader` in case a `mask` is given ([#8312](https://github.com/pyg-team/pytorch_geometric/pull/8312))
 - Respect current device when deep-copying `Linear` layers ([#8311](https://github.com/pyg-team/pytorch_geometric/pull/8311))
diff --git a/torch_geometric/explain/algorithm/graphmask_explainer.py b/torch_geometric/explain/algorithm/graphmask_explainer.py
index 912026ce6c56..089fe7659a6e 100644
--- a/torch_geometric/explain/algorithm/graphmask_explainer.py
+++ b/torch_geometric/explain/algorithm/graphmask_explainer.py
@@ -526,12 +526,6 @@ def _explain(
                 if i == 0:
                     edge_weight = sampling_weights
                 else:
-                    if edge_weight.size(-1) != sampling_weights.size(-1):
-                        sampling_weights = F.pad(
-                            input=sampling_weights,
-                            pad=(0, edge_weight.size(-1) -
-                                 sampling_weights.size(-1), 0, 0),
-                            mode='constant', value=0)
                     edge_weight = torch.cat((edge_weight, sampling_weights), 0)
                 if self.log:
                     pbar.update(1)