diff --git a/qiskit_ibm_runtime/utils/backend_converter.py b/qiskit_ibm_runtime/utils/backend_converter.py
index 3db605d100..4f7051883a 100644
--- a/qiskit_ibm_runtime/utils/backend_converter.py
+++ b/qiskit_ibm_runtime/utils/backend_converter.py
@@ -25,6 +25,8 @@
     ECRGate,
     CZGate,
 )
+from qiskit.circuit.controlflow import CONTROL_FLOW_OP_NAMES
+from qiskit.circuit import IfElseOp, WhileLoopOp, ForLoopOp, SwitchCaseOp
 from qiskit.circuit.parameter import Parameter
 from qiskit.circuit.delay import Delay
 from qiskit.circuit.gate import Gate
@@ -56,6 +58,10 @@ def convert_to_target(
         "reset": Reset(),
         "ecr": ECRGate(),
         "cz": CZGate(),
+        "if_else": IfElseOp,
+        "while_loop": WhileLoopOp,
+        "for_loop": ForLoopOp,
+        "switch_case": SwitchCaseOp,
     }
     custom_gates = {}
     target = None
@@ -128,6 +134,10 @@ def convert_to_target(
         target.min_length = configuration.timing_constraints.get("min_length")
         target.pulse_alignment = configuration.timing_constraints.get("pulse_alignment")
         target.acquire_alignment = configuration.timing_constraints.get("acquire_alignment")
+    supported_instructions = set(getattr(configuration, "supported_instructions", []))
+    control_flow_ops = CONTROL_FLOW_OP_NAMES.intersection(supported_instructions)
+    for op in control_flow_ops:
+        target.add_instruction(name_mapping[op], name=op)
     # If pulse defaults exists use that as the source of truth
     if defaults is not None:
         faulty_qubits = set()
diff --git a/releasenotes/notes/fix-control-flow-d5a61dd5647acb42.yaml b/releasenotes/notes/fix-control-flow-d5a61dd5647acb42.yaml
new file mode 100644
index 0000000000..0031db5cc7
--- /dev/null
+++ b/releasenotes/notes/fix-control-flow-d5a61dd5647acb42.yaml
@@ -0,0 +1,6 @@
+---
+fixes:
+  - |
+    Fixed an issue with the :attr:`.IBMBackend.target` where it would
+    incorrectly exclude supported control flow operations (:class:`.IfElseOp`,
+    :class:`.WhileLoop`, etc.) if a given backend supported them.
diff --git a/test/unit/test_backend.py b/test/unit/test_backend.py
index 3eda26ed2b..754236e988 100644
--- a/test/unit/test_backend.py
+++ b/test/unit/test_backend.py
@@ -16,11 +16,18 @@
 import warnings
 
 from qiskit import transpile, qasm3, QuantumCircuit
-from qiskit.providers.models import BackendStatus
+from qiskit.circuit import IfElseOp
+from qiskit.providers.models import (
+    BackendStatus,
+    BackendConfiguration,
+    BackendProperties,
+    PulseDefaults,
+)
 
 from qiskit_ibm_runtime.exceptions import IBMBackendValueError
-from qiskit_ibm_runtime.fake_provider import FakeManila
+from qiskit_ibm_runtime.fake_provider import FakeManila, FakeSherbrooke
 from qiskit_ibm_runtime.ibm_backend import IBMBackend
+from qiskit_ibm_runtime.utils.backend_converter import convert_to_target
 
 from ..ibm_test_case import IBMTestCase
 from ..utils import (
@@ -305,3 +312,17 @@ def test_too_many_circuits(self):
             f"Number of circuits, {max_circs+1} exceeds the maximum for this backend, {max_circs}",
             str(err.exception),
         )
+
+    def test_control_flow_converter(self):
+        """Test that control flow instructions are properly added to the target."""
+        backend = FakeSherbrooke()
+        backend._get_conf_dict_from_json()
+        backend._set_props_dict_from_json()
+        backend._set_defs_dict_from_json()
+        target = convert_to_target(
+            BackendConfiguration.from_dict(backend._conf_dict),
+            BackendProperties.from_dict(backend._props_dict),
+            PulseDefaults.from_dict(backend._defs_dict),
+        )
+        self.assertTrue(target.instruction_supported("if_else", ()))
+        self.assertTrue(target.instruction_supported(operation_class=IfElseOp))