diff --git a/qiskit/transpiler/passes/scheduling/padding/dynamical_decoupling.py b/qiskit/transpiler/passes/scheduling/padding/dynamical_decoupling.py
index 8c3ea87c8578..0e351161f7df 100644
--- a/qiskit/transpiler/passes/scheduling/padding/dynamical_decoupling.py
+++ b/qiskit/transpiler/passes/scheduling/padding/dynamical_decoupling.py
@@ -20,7 +20,7 @@
 from qiskit.circuit.delay import Delay
 from qiskit.circuit.library.standard_gates import IGate, UGate, U3Gate
 from qiskit.circuit.reset import Reset
-from qiskit.dagcircuit import DAGCircuit, DAGNode, DAGInNode, DAGOpNode
+from qiskit.dagcircuit import DAGCircuit, DAGNode, DAGInNode, DAGOpNode, DAGOutNode
 from qiskit.quantum_info.operators.predicates import matrix_equal
 from qiskit.synthesis.one_qubit import OneQubitEulerDecomposer
 from qiskit.transpiler.exceptions import TranspilerError
@@ -331,8 +331,7 @@ def _pad(
         if time_interval % self._alignment != 0:
             raise TranspilerError(
                 f"Time interval {time_interval} is not divisible by alignment {self._alignment} "
-                f"between DAGNode {prev_node.name} on qargs {prev_node.qargs} and {next_node.name} "
-                f"on qargs {next_node.qargs}."
+                f"between {_format_node(prev_node)} and {_format_node(next_node)}."
             )
 
         if not self.__is_dd_qubit(dag.qubits.index(qubit)):
@@ -430,3 +429,10 @@ def _resolve_params(gate: Gate) -> tuple:
             else:
                 params.append(p)
         return tuple(params)
+
+
+def _format_node(node: DAGNode) -> str:
+    """Util to format the DAGNode, DAGInNode, and DAGOutNode."""
+    if isinstance(node, (DAGInNode, DAGOutNode)):
+        return f"{node.__class__.__name__} on qarg {node.wire}"
+    return f"DAGNode {node.name} on qargs {node.qargs}"
diff --git a/releasenotes/notes/fix-dd-misalignment-msg-76fe16e5eb4ae670.yaml b/releasenotes/notes/fix-dd-misalignment-msg-76fe16e5eb4ae670.yaml
new file mode 100644
index 000000000000..4634fe48ae9b
--- /dev/null
+++ b/releasenotes/notes/fix-dd-misalignment-msg-76fe16e5eb4ae670.yaml
@@ -0,0 +1,7 @@
+---
+fixes:
+  - |
+    Fixed a bug in :class:`.PadDynamicalDecoupling`, which previously
+    did not correctly display the error message that a delay is not
+    pulse-aligned, if the previous or following node was an input/output
+    node. Now, the error message is correctly displayed.
diff --git a/test/python/transpiler/test_dynamical_decoupling.py b/test/python/transpiler/test_dynamical_decoupling.py
index 5f11ede3a3e8..38c5c3c2d4ab 100644
--- a/test/python/transpiler/test_dynamical_decoupling.py
+++ b/test/python/transpiler/test_dynamical_decoupling.py
@@ -1051,6 +1051,23 @@ def test_paramaterized_global_phase(self):
 
         self.assertEqual(qc.global_phase + np.pi, pm.run(qc).global_phase)
 
+    def test_misalignment_at_boundaries(self):
+        """Test the correct error message is raised for misalignments at In/Out nodes."""
+        # a circuit where the previous node is DAGInNode, and the next DAGOutNode
+        circuit = QuantumCircuit(1)
+        circuit.delay(101)
+
+        dd_sequence = [XGate(), XGate()]
+        pm = PassManager(
+            [
+                ALAPScheduleAnalysis(self.durations),
+                PadDynamicalDecoupling(self.durations, dd_sequence, pulse_alignment=2),
+            ]
+        )
+
+        with self.assertRaises(TranspilerError):
+            _ = pm.run(circuit)
+
 
 if __name__ == "__main__":
     unittest.main()