diff --git a/circuit_knitting/utils/transforms.py b/circuit_knitting/utils/transforms.py
index 2849d093e..68579da24 100644
--- a/circuit_knitting/utils/transforms.py
+++ b/circuit_knitting/utils/transforms.py
@@ -172,6 +172,8 @@ def _partition_labels_from_circuit(
         # Determine which qubit wires are idle/unused
         idle_wires = set(range(circuit.num_qubits))
         for instruction in circuit.data:
+            if instruction.operation.name == "barrier":
+                continue
             for q1 in instruction.qubits:
                 q1_id = circuit.find_bit(q1).index
                 idle_wires.discard(q1_id)
diff --git a/test/utils/test_transforms.py b/test/utils/test_transforms.py
index 181a7b27f..d082fc95c 100644
--- a/test/utils/test_transforms.py
+++ b/test/utils/test_transforms.py
@@ -262,6 +262,48 @@ def test_separate_circuit(self):
                 [("A", 0), ("B", 0), ("C", 0)], separated_circuits.qubit_map
             )
 
+        with self.subTest("barriers are ignored"):
+            qreg = QuantumRegister(3)
+            circuit = QuantumCircuit(qreg)
+            circuit.h(0)
+            circuit.x(0)
+            circuit.barrier(0)
+            circuit.x(1)
+            circuit.h(1)
+            circuit.y(2)
+            circuit.h(2)
+
+            separated_circuits = separate_circuit(circuit, partition_labels="ABC")
+
+            compare1 = QuantumCircuit(1)
+            compare1.h(0)
+            compare1.x(0)
+            compare2 = QuantumCircuit(1)
+            compare2.x(0)
+            compare2.h(0)
+            compare3 = QuantumCircuit(1)
+            compare3.y(0)
+            compare3.h(0)
+
+            for i, operation in enumerate(compare1.data):
+                self.assertEqual(
+                    operation.operation.name,
+                    separated_circuits.subcircuits["A"].data[i].operation.name,
+                )
+            for i, operation in enumerate(compare2.data):
+                self.assertEqual(
+                    operation.operation.name,
+                    separated_circuits.subcircuits["B"].data[i].operation.name,
+                )
+            for i, operation in enumerate(compare3.data):
+                self.assertEqual(
+                    operation.operation.name,
+                    separated_circuits.subcircuits["C"].data[i].operation.name,
+                )
+            self.assertEqual(
+                [("A", 0), ("B", 0), ("C", 0)], separated_circuits.qubit_map
+            )
+
         with self.subTest("Test bit mapping with partition labels"):
             # Prepare a HWEA and add some measurements to clbits in a random order
             circuit = prepare_hwea()