diff --git a/qiskit/pulse/compiler/basepasses.py b/qiskit/pulse/compiler/basepasses.py
index 8e1c40443ae..e362935c181 100644
--- a/qiskit/pulse/compiler/basepasses.py
+++ b/qiskit/pulse/compiler/basepasses.py
@@ -46,6 +46,16 @@ def run(
     ) -> IrBlock:
         pass
 
+    def __hash__(self) -> int:
+        warnings.warn(
+            f"{self.__class__} does not explicitly define a protocol to calculate hash. "
+            "This pass created the hash only by considering the class name. "
+            "Qiskit flow controller assumes passes with the identical hash are idempotent, "
+            "and it may skip execution of the other passes in the pipeline.",
+            RuntimeWarning,
+        )
+        return hash((self.__class__.__name__,))
+
     def __eq__(self, other):
         warnings.warn(
             f"{self.__class__} does not explicitly define a protocol to evaluate equality. "
@@ -83,6 +93,16 @@ def run(
     ) -> None:
         pass
 
+    def __hash__(self) -> int:
+        warnings.warn(
+            f"{self.__class__} does not explicitly define a protocol to calculate hash. "
+            "This pass created the hash only by considering the class name. "
+            "Qiskit flow controller assumes passes with the identical hash are idempotent, "
+            "and it may skip execution of the other passes in the pipeline.",
+            RuntimeWarning,
+        )
+        return hash((self.__class__.__name__,))
+
     def __eq__(self, other):
         warnings.warn(
             f"{self.__class__} does not explicitly define a protocol to evaluate equality. "
diff --git a/qiskit/pulse/compiler/passmanager.py b/qiskit/pulse/compiler/passmanager.py
index b86f36963dd..6179a201bcc 100644
--- a/qiskit/pulse/compiler/passmanager.py
+++ b/qiskit/pulse/compiler/passmanager.py
@@ -55,11 +55,12 @@ def _passmanager_frontend(
     ) -> IrBlock:
 
         def _wrap_recursive(_prog):
-            _ret = IrBlock(alignment=input_program.alignment_context)
+            _ret = IrBlock(alignment=_prog.alignment_context)
             for _elm in _prog.blocks:
                 if isinstance(_elm, ScheduleBlock):
-                    return _wrap_recursive(_elm)
-                _ret.add_element(IrInstruction(instruction=_elm))
+                    _ret.add_element(_wrap_recursive(_elm))
+                else:
+                    _ret.add_element(IrInstruction(instruction=_elm))
             return _ret
 
         return _wrap_recursive(input_program)
@@ -148,11 +149,12 @@ def _passmanager_backend(
     ) -> ScheduleBlock:
 
         def _unwrap_recursive(_prog):
-            _ret = ScheduleBlock(alignment_context=passmanager_ir.alignment)
+            _ret = ScheduleBlock(alignment_context=_prog.alignment)
             for _elm in _prog.elements:
                 if isinstance(_elm, IrBlock):
-                    return _unwrap_recursive(_elm)
-                _ret.append(_elm.instruction, inplace=True)
+                    _ret.append(_unwrap_recursive(_elm), inplace=True)
+                else:
+                    _ret.append(_elm.instruction, inplace=True)
             return _ret
 
         out_block = _unwrap_recursive(passmanager_ir)
diff --git a/test/python/pulse/test_compile.py b/test/python/pulse/test_compile.py
index 697cbd3b5a5..c0464e1f03c 100644
--- a/test/python/pulse/test_compile.py
+++ b/test/python/pulse/test_compile.py
@@ -13,18 +13,35 @@
 """A test cases for pulse compilation."""
 
 from qiskit.pulse.compiler import BlockTranspiler
+from qiskit.pulse.compiler.basepasses import TransformationPass
+from qiskit.pulse.ir.ir import IrBlock
+from qiskit.providers.fake_provider import GenericBackendV2
 
 from test import QiskitTestCase  # pylint: disable=wrong-import-order
 from . import _dummy_programs as schedule_lib
 
 
+class _DummyPass(TransformationPass):
+    """A test pass that doesn't perform any transformation."""
+
+    def run(self, passmanager_ir: IrBlock) -> IrBlock:
+        return passmanager_ir
+
+    def __hash__(self) -> int:
+        return hash((self.__class__.__name__,))
+
+    def __eq__(self, other):
+        return self.__class__.__name == other.__class__.name__
+
+
 class TestCompiler(QiskitTestCase):
     """Test case for pulse compiler."""
 
     def test_roundtrip_simple(self):
         """Test just returns the input program."""
         # Just convert an input to PulseIR and convert it back to ScheduleBlock.
-        pm = BlockTranspiler()
+        backend = GenericBackendV2(2)
+        pm = BlockTranspiler([_DummyPass(backend.target)])
 
         in_prog = schedule_lib.play_gaussian()
         out_prog = pm.run(pulse_programs=in_prog)
@@ -33,7 +50,8 @@ def test_roundtrip_simple(self):
     def test_roundtrip_nested(self):
         """Test just returns the input program."""
         # Just convert an input to PulseIR and convert it back to ScheduleBlock.
-        pm = BlockTranspiler()
+        backend = GenericBackendV2(2)
+        pm = BlockTranspiler([_DummyPass(backend.target)])
 
         in_prog = schedule_lib.play_and_inner_block_sequential()
         out_prog = pm.run(pulse_programs=in_prog)