diff --git a/qiskit_ibm_runtime/transpiler/passes/scheduling/block_base_padder.py b/qiskit_ibm_runtime/transpiler/passes/scheduling/block_base_padder.py
index e065b0606a..ea5bed527c 100644
--- a/qiskit_ibm_runtime/transpiler/passes/scheduling/block_base_padder.py
+++ b/qiskit_ibm_runtime/transpiler/passes/scheduling/block_base_padder.py
@@ -363,6 +363,8 @@ def _visit_block(
         prev_node = self._prev_node
         self._prev_node = None
         prev_wire_map, self._wire_map = self._wire_map, wire_map
+        prev_idle_after = self._idle_after
+        prev_current_block_idx = self._current_block_idx
 
         prev_block_dag = self._block_dag
         self._block_dag = new_block_dag = self._empty_dag_like(
@@ -394,13 +396,15 @@ def _visit_block(
         # Edge-case: Add a barrier if the final node is a fast-path
         if self._prev_node in self._fast_path_nodes:
             self._add_block_terminating_barrier(
-                prev_block_duration, prev_block_idx, self._prev_node, force=True
+                prev_block_idx, prev_block_duration, self._prev_node, force=True
             )
 
         # Pop the previous block dag off the stack restoring it
         self._block_dag = prev_block_dag
         self._prev_node = prev_node
         self._wire_map = prev_wire_map
+        self._idle_after = prev_idle_after
+        self._current_block_idx = prev_current_block_idx
 
         return new_block_dag
 
@@ -463,9 +467,9 @@ def _will_use_fast_path(self, node: DAGNode) -> bool:
     def _visit_control_flow_op(self, node: DAGNode) -> None:
         """Visit a control-flow node to pad."""
         # Control-flow terminator ends scheduling of block currently
-        block_idx, t0 = self._node_start_time[node]
-        self._terminate_block(t0, block_idx)
-        self._add_block_terminating_barrier(block_idx, t0, node)
+        scheduled_block_idx, t0 = self._node_start_time[node]
+        self._terminate_block(t0, scheduled_block_idx)
+        self._add_block_terminating_barrier(scheduled_block_idx, t0, node)
 
         # Only pad non-fast path nodes
         fast_path_node = node in self._fast_path_nodes
@@ -480,8 +484,8 @@ def _visit_control_flow_op(self, node: DAGNode) -> None:
         # We resolve this here by extracting the cached dag blocks that were
         # stored by the scheduling pass.
         new_node_block_dags = []
-        for block_idx, _ in enumerate(node.op.blocks):
-            block_dag = self._node_block_dags[node][block_idx]
+        for body_idx, _ in enumerate(node.op.blocks):
+            block_dag = self._node_block_dags[node][body_idx]
             inner_wire_map = {
                 inner: outer
                 for outer, inner in zip(
@@ -513,7 +517,7 @@ def _visit_control_flow_op(self, node: DAGNode) -> None:
         else:
             padded_qubits = self._block_dag.qubits
         self._apply_scheduled_op(
-            block_idx,
+            scheduled_block_idx,
             t0,
             new_control_flow_op,
             padded_qubits,
diff --git a/release-notes/unreleased/3077.bug.rst b/release-notes/unreleased/3077.bug.rst
new file mode 100644
index 0000000000..114938f006
--- /dev/null
+++ b/release-notes/unreleased/3077.bug.rst
@@ -0,0 +1,6 @@
+Fixed control-flow padding in :class:`.BlockBasePadder` so nested block traversal no
+longer leaks timing state into the parent block. Rebuilt control-flow operations now
+retain their scheduled block index, and barriers after final fast-path operations use
+the correct block index and start time. This prevents incorrect scheduling metadata and
+padding when dynamic circuits contain nested or multi-branch control flow
+(:issue:`3077`; idle-qubit detection in :issue:`3005` remains separate).
diff --git a/test/unit/transpiler/passes/scheduling/test_scheduler.py b/test/unit/transpiler/passes/scheduling/test_scheduler.py
index 0b175676f7..de99d46b14 100644
--- a/test/unit/transpiler/passes/scheduling/test_scheduler.py
+++ b/test/unit/transpiler/passes/scheduling/test_scheduler.py
@@ -14,9 +14,10 @@
 
 from ddt import data, ddt
 from qiskit import ClassicalRegister, QuantumCircuit, QuantumRegister, transpile
-from qiskit.circuit import Delay, Parameter
+from qiskit.circuit import ControlFlowOp, Delay, Parameter
 from qiskit.circuit.library import CXGate, Measure, Reset, RZGate, XGate
 from qiskit.converters import circuit_to_dag
+from qiskit.dagcircuit import DAGCircuit
 from qiskit.transpiler.exceptions import TranspilerError
 from qiskit.transpiler.passmanager import PassManager
 from qiskit.transpiler.target import InstructionProperties, Target
@@ -1178,6 +1179,89 @@ def test_back_to_back_if_test(self, use_target):
 
         self.assertEqual(expected, scheduled)
 
+    def test_padding_preserves_control_flow_block_indices(self):
+        """Test that rebuilding control-flow ops preserves their scheduled block indices."""
+        target = Target(num_qubits=3, dt=1)
+        target.add_instruction(
+            XGate(),
+            {(qubit,): InstructionProperties(duration=200) for qubit in range(3)},
+        )
+        target.add_instruction(
+            Measure(),
+            {(qubit,): InstructionProperties(duration=1000) for qubit in range(3)},
+        )
+
+        circuit = QuantumCircuit(3, 1)
+        circuit.measure(0, 0)
+        with circuit.if_test((0, True)) as else_:
+            circuit.x(1)
+        with else_:
+            circuit.x(2)
+        with circuit.if_test((0, True)) as else_:
+            circuit.x(2)
+        with else_:
+            circuit.x(1)
+
+        scheduler = PassManager([ASAPScheduleAnalysis(target=target)])
+        scheduler.run(circuit)
+        expected = [
+            start_time
+            for node, start_time in scheduler.property_set["node_start_time"].items()
+            if isinstance(node.op, ControlFlowOp)
+        ]
+
+        scheduler_and_padder = PassManager(
+            [
+                ASAPScheduleAnalysis(target=target),
+                PadDelay(target=target, schedule_idle_qubits=True),
+            ]
+        )
+        scheduler_and_padder.run(circuit)
+        actual = [
+            start_time
+            for node, start_time in scheduler_and_padder.property_set["node_start_time"].items()
+            if isinstance(node.op, ControlFlowOp)
+        ]
+
+        self.assertEqual(expected, actual)
+
+    def test_nested_block_visit_restores_parent_timing_state(self):
+        """Test nested timing state restoration and final fast-path barrier placement."""
+        padder = PadDelay(target=Target(num_qubits=1, dt=1))
+        parent_qubit = QuantumCircuit(1).qubits[0]
+        parent_idle_after = {parent_qubit: 10}
+        padder._idle_after = parent_idle_after
+        padder._current_block_idx = 7
+        padder._prev_node = None
+        padder._wire_map = {}
+        padder._block_dag = DAGCircuit()
+        padder._block_duration = 0
+        padder._block_ordering_callable = lambda _: []
+
+        nested_dag = DAGCircuit()
+        padder._empty_dag_like = lambda *args, **kwargs: nested_dag
+        fast_path_node = object()
+        padder._fast_path_nodes = {fast_path_node}
+        terminating_barrier_args = []
+
+        def mutate_nested_timing_state(block_duration, block_idx):
+            del block_duration, block_idx
+            padder._idle_after = {parent_qubit: 20}
+            padder._current_block_idx = 11
+            padder._prev_node = fast_path_node
+
+        def record_terminating_barrier(block_idx, time, current_node, force=False):
+            terminating_barrier_args.append((block_idx, time, current_node, force))
+
+        padder._terminate_block = mutate_nested_timing_state
+        padder._add_block_terminating_barrier = record_terminating_barrier
+
+        padder._visit_block(nested_dag, {})
+
+        self.assertEqual(terminating_barrier_args, [(7, 0, fast_path_node, True)])
+        self.assertIs(padder._idle_after, parent_idle_after)
+        self.assertEqual(padder._current_block_idx, 7)
+
     @data(True, False)
     def test_nested_control_scheduling(self, use_target):
         """Test scheduling of nested control-flow."""