diff --git a/qiskit/providers/backend_compat.py b/qiskit/providers/backend_compat.py
index 3d54656545b4..fcd82765eeb6 100644
--- a/qiskit/providers/backend_compat.py
+++ b/qiskit/providers/backend_compat.py
@@ -21,7 +21,7 @@
 from qiskit.providers.backend import QubitProperties
 from qiskit.providers.models.backendconfiguration import BackendConfiguration
 from qiskit.providers.models.backendproperties import BackendProperties
-
+from qiskit.circuit.controlflow import CONTROL_FLOW_OP_NAMES
 from qiskit.providers.models.pulsedefaults import PulseDefaults
 from qiskit.providers.options import Options
 from qiskit.providers.exceptions import BackendPropertyError
@@ -92,8 +92,12 @@ def convert_to_target(
 
     # Create instruction property placeholder from backend configuration
     basis_gates = set(getattr(configuration, "basis_gates", []))
+    supported_instructions = set(getattr(configuration, "supported_instructions", []))
     gate_configs = {gate.name: gate for gate in configuration.gates}
-    all_instructions = set.union(basis_gates, set(required))
+    all_instructions = set.union(
+        basis_gates, set(required), supported_instructions.intersection(CONTROL_FLOW_OP_NAMES)
+    )
+
     inst_name_map = {}  # type: Dict[str, Instruction]
 
     faulty_ops = set()
diff --git a/releasenotes/notes/fix-control-flow-convert-to-target-ae838418a7ad2a20.yaml b/releasenotes/notes/fix-control-flow-convert-to-target-ae838418a7ad2a20.yaml
new file mode 100644
index 000000000000..be29520fad89
--- /dev/null
+++ b/releasenotes/notes/fix-control-flow-convert-to-target-ae838418a7ad2a20.yaml
@@ -0,0 +1,9 @@
+---
+fixes:
+  - |
+    Fixed an issue with the :func:`.convert_to_target` where the converter
+    would incorrectly ignore control flow instructions if they were specified
+    in the :attr:`.BackendConfiguration.supported_instructions` attribute which
+    is the typical location that control flow instructions are specified in a
+    :class:`.BackendConfiguration` object.
+    Fixed `#11872 <https://github.com/Qiskit/qiskit/issues/11872>`__.
diff --git a/test/python/providers/test_fake_backends.py b/test/python/providers/test_fake_backends.py
index f4f42e839f4d..101e35acc8e1 100644
--- a/test/python/providers/test_fake_backends.py
+++ b/test/python/providers/test_fake_backends.py
@@ -34,7 +34,7 @@
     FakeOpenPulse2Q,
     GenericBackendV2,
 )
-from qiskit.providers.backend_compat import BackendV2Converter
+from qiskit.providers.backend_compat import BackendV2Converter, convert_to_target
 from qiskit.providers.models.backendproperties import BackendProperties
 from qiskit.providers.backend import BackendV2
 from qiskit.providers.models import GateConfig
@@ -709,3 +709,59 @@ def test_faulty_full_path_transpile_connected_cmap(self, opt_level):
         tqc = transpile(qc, v2_backend, seed_transpiler=433, optimization_level=opt_level)
         connections = [tuple(sorted(tqc.find_bit(q).index for q in x.qubits)) for x in tqc.data]
         self.assertNotIn((0, 1), connections)
+
+    def test_convert_to_target_control_flow(self):
+        backend = Fake27QPulseV1()
+        properties = backend.properties()
+        configuration = backend.configuration()
+        configuration.supported_instructions = [
+            "cx",
+            "id",
+            "delay",
+            "measure",
+            "reset",
+            "rz",
+            "sx",
+            "x",
+            "if_else",
+            "for_loop",
+            "switch_case",
+        ]
+        defaults = backend.defaults()
+        target = convert_to_target(configuration, properties, defaults)
+        self.assertTrue(target.instruction_supported("if_else", ()))
+        self.assertFalse(target.instruction_supported("while_loop", ()))
+        self.assertTrue(target.instruction_supported("for_loop", ()))
+        self.assertTrue(target.instruction_supported("switch_case", ()))
+
+    def test_convert_unrelated_supported_instructions(self):
+        backend = Fake27QPulseV1()
+        properties = backend.properties()
+        configuration = backend.configuration()
+        configuration.supported_instructions = [
+            "cx",
+            "id",
+            "delay",
+            "measure",
+            "reset",
+            "rz",
+            "sx",
+            "x",
+            "play",
+            "u2",
+            "u3",
+            "u1",
+            "shiftf",
+            "acquire",
+            "setf",
+            "if_else",
+            "for_loop",
+            "switch_case",
+        ]
+        defaults = backend.defaults()
+        target = convert_to_target(configuration, properties, defaults)
+        self.assertTrue(target.instruction_supported("if_else", ()))
+        self.assertFalse(target.instruction_supported("while_loop", ()))
+        self.assertTrue(target.instruction_supported("for_loop", ()))
+        self.assertTrue(target.instruction_supported("switch_case", ()))
+        self.assertFalse(target.instruction_supported("u3", (0,)))