diff --git a/qiskit/transpiler/passes/optimization/elide_permutations.py b/qiskit/transpiler/passes/optimization/elide_permutations.py
index ca6902f15b43..81d0aa8bf1ae 100644
--- a/qiskit/transpiler/passes/optimization/elide_permutations.py
+++ b/qiskit/transpiler/passes/optimization/elide_permutations.py
@@ -96,8 +96,8 @@ def _apply_mapping(qargs):
             elif isinstance(node.op, PermutationGate):
                 starting_indices = [qubit_mapping[dag.find_bit(qarg).index] for qarg in node.qargs]
                 pattern = node.op.params[0]
-                pattern_indices = [qubit_mapping[idx] for idx in pattern]
-                for i, j in zip(starting_indices, pattern_indices):
+                updated_indices = [starting_indices[idx] for idx in pattern]
+                for i, j in zip(starting_indices, updated_indices):
                     qubit_mapping[i] = j
         input_qubit_mapping = {qubit: index for index, qubit in enumerate(dag.qubits)}
         self.property_set["original_layout"] = Layout(input_qubit_mapping)
diff --git a/releasenotes/notes/fix-elide-permutations-1b9e1d10c3abb2a4.yaml b/releasenotes/notes/fix-elide-permutations-1b9e1d10c3abb2a4.yaml
new file mode 100644
index 000000000000..156960eb7c19
--- /dev/null
+++ b/releasenotes/notes/fix-elide-permutations-1b9e1d10c3abb2a4.yaml
@@ -0,0 +1,5 @@
+---
+fixes:
+  - |
+    Fixed a bug in the transpiler pass :class:`~.ElidePermutations` where the
+    qubit mapping was not updated correctly in the presence of :class:`.PermutationGate`\s.
diff --git a/test/python/transpiler/test_elide_permutations.py b/test/python/transpiler/test_elide_permutations.py
index c96b5ca32d89..6f3051cec0d6 100644
--- a/test/python/transpiler/test_elide_permutations.py
+++ b/test/python/transpiler/test_elide_permutations.py
@@ -207,6 +207,37 @@ def test_permutation_in_middle(self):
         res = self.swap_pass(qc)
         self.assertEqual(res, expected)
 
+    def test_partial_permutation_in_middle(self):
+        """Test with a permutation gate in the middle of a circuit,
+        with the permutation gate defined only on a subset of qubits.
+        """
+        qc = QuantumCircuit(5)
+        qc.cx(0, 1)
+        qc.append(PermutationGate([1, 2, 0]), [0, 2, 4])
+        qc.cx(2, 3)
+
+        # The permutation corresponding to the permutation gate maps
+        #   2 -> 0, 4 -> 2, 0 -> 4, and 1 -> 1, 3 -> 3.
+        # Instead of the permutation gate, we can relabel the qubits
+        #   0 -> 2, 1 -> 1, 2 -> 4, 3 -> 3, 4 -> 2.
+        # Hence cx(2, 3) becomes cx(4, 3).
+        expected = QuantumCircuit(5)
+        expected.cx(0, 1)
+        expected.cx(4, 3)
+
+        pass_ = ElidePermutations()
+        res = pass_(qc)
+
+        # Make sure that the pass removes the permutation gate and remaps
+        # the following gate
+        self.assertEqual(res, expected)
+
+        # Make sure that the transpiled circuit *with* the final permutation
+        # is equivalent to the original circuit
+        perm = pass_.property_set["virtual_permutation_layout"].to_permutation(qc.qubits)
+        res.append(PermutationGate(perm), [0, 1, 2, 3, 4])
+        self.assertEqual(Operator(res), Operator(qc))
+
     def test_permutation_at_beginning(self):
         """Test permutation in beginning of bell is elided."""
         qc = QuantumCircuit(3, 3)