diff --git a/qiskit_aer/backends/aer_compiler.py b/qiskit_aer/backends/aer_compiler.py
index a0c75247cc..846eb10052 100644
--- a/qiskit_aer/backends/aer_compiler.py
+++ b/qiskit_aer/backends/aer_compiler.py
@@ -259,6 +259,9 @@ def _inline_for_loop_op(self, instruction, parent, bit_map):
         """inline for_loop body while iterating its indexset"""
         qargs = [bit_map[q] for q in instruction.qubits]
         cargs = [bit_map[c] for c in instruction.clbits]
+        # to avoid wrong topological sorting of command with "empty" block
+        if len(qargs) == 0:
+            qargs = parent.qubits
         indexset, loop_parameter, body = instruction.operation.params
         inner_bit_map = {
             inner: bit_map[outer]
@@ -320,6 +323,9 @@ def _inline_while_loop_op(self, instruction, parent, bit_map):
         )
         qargs = [bit_map[q] for q in instruction.qubits]
         cargs = [bit_map[c] for c in instruction.clbits]
+        # to avoid wrong topological sorting of command with "empty" block
+        if len(qargs) == 0:
+            qargs = parent.qubits
 
         if isinstance(condition_tuple, Expr):
             mark_cargs = self._list_clbit_from_expr(bit_map, condition_tuple)
@@ -371,6 +377,13 @@ def _inline_if_else_op(self, instruction, continue_label, break_label, parent, b
 
         qargs = [bit_map[q] for q in instruction.qubits]
         cargs = [bit_map[c] for c in instruction.clbits]
+        # to avoid wrong topological sorting of command with "empty" block
+        if len(qargs) == 0:
+            qargs = parent.qubits
+
+        # to avoid wrong topological sorting of command with "empty" block
+        if len(qargs) == 0:
+            qargs = parent.qubits
 
         if isinstance(condition_tuple, Expr):
             mark_cargs = self._list_clbit_from_expr(bit_map, condition_tuple)
@@ -439,6 +452,9 @@ def _inline_switch_case_op(self, instruction, continue_label, break_label, paren
 
         qargs = [bit_map[q] for q in instruction.qubits]
         cargs = [bit_map[c] for c in instruction.clbits]
+        # to avoid wrong topological sorting of command with "empty" block
+        if len(qargs) == 0:
+            qargs = parent.qubits
 
         if isinstance(instruction.operation.target, Clbit):
             target_clbits = {bit_map[instruction.operation.target]}
diff --git a/releasenotes/notes/fix_infinite_run_on_empty_conditional-d9e6d31ffa1c3bc3.yaml b/releasenotes/notes/fix_infinite_run_on_empty_conditional-d9e6d31ffa1c3bc3.yaml
new file mode 100644
index 0000000000..10bcad90b8
--- /dev/null
+++ b/releasenotes/notes/fix_infinite_run_on_empty_conditional-d9e6d31ffa1c3bc3.yaml
@@ -0,0 +1,7 @@
+---
+fixes:
+  - |
+    Using a conditional with empty body caused the transpile run to
+    mix the order of gates in the circuit, leading sometimes to infinite
+    simulations.
+    This fix ensures that the order of gates is preserved.
diff --git a/test/terra/backends/aer_simulator/test_conditional.py b/test/terra/backends/aer_simulator/test_conditional.py
index ec33fd404b..56dc936781 100644
--- a/test/terra/backends/aer_simulator/test_conditional.py
+++ b/test/terra/backends/aer_simulator/test_conditional.py
@@ -16,7 +16,7 @@
 from test.terra.reference import ref_conditionals
 from test.terra.backends.simulator_test_case import SimulatorTestCase, supported_methods
 
-from qiskit import QuantumCircuit
+from qiskit import QuantumCircuit, ClassicalRegister
 from qiskit.circuit.library import DiagonalGate
 
 
@@ -380,3 +380,23 @@ def test_conditional_diagonal(self):
 
         self.assertNotEqual(result.data(circuit)["base"], result.data(circuit0)["diff"])
         self.assertEqual(result.data(circuit)["base"], result.data(circuit1)["equal"])
+
+
+class TestConditionalErrors(SimulatorTestCase):
+    def test_infinite_run_error(self):
+        backend = self.backend(method="statevector", device="CPU")
+        backend.set_options(max_parallel_experiments=0)
+
+        main_circ = QuantumCircuit(1)
+        creg_0 = ClassicalRegister(1)
+        main_circ.add_register(creg_0)
+        main_circ.measure(0, creg_0[0])
+        main_circ.x(0)
+        with main_circ.if_test((creg_0[0], 0)) as else_1:
+            pass
+        with else_1:
+            pass
+        main_circ.measure_active()
+
+        result = backend.run(main_circ, shots=1).result()
+        self.assertSuccess(result)