diff --git a/qiskit/quantum_info/operators/symplectic/pauli.py b/qiskit/quantum_info/operators/symplectic/pauli.py
index 1ccecc04a6c0..8187c1ee41e6 100644
--- a/qiskit/quantum_info/operators/symplectic/pauli.py
+++ b/qiskit/quantum_info/operators/symplectic/pauli.py
@@ -736,8 +736,11 @@ def apply_layout(
             n_qubits = num_qubits
         if layout is None:
             layout = list(range(self.num_qubits))
-        elif any(x >= n_qubits for x in layout):
-            raise QiskitError("Provided layout contains indices outside the number of qubits.")
+        else:
+            if any(x < 0 or x >= n_qubits for x in layout):
+                raise QiskitError("Provided layout contains indices outside the number of qubits.")
+            if len(set(layout)) != len(layout):
+                raise QiskitError("Provided layout contains duplicate indices.")
         new_op = type(self)("I" * n_qubits)
         return new_op.compose(self, qargs=layout)
 
diff --git a/qiskit/quantum_info/operators/symplectic/sparse_pauli_op.py b/qiskit/quantum_info/operators/symplectic/sparse_pauli_op.py
index dffe5b2396b2..cf51579bef8f 100644
--- a/qiskit/quantum_info/operators/symplectic/sparse_pauli_op.py
+++ b/qiskit/quantum_info/operators/symplectic/sparse_pauli_op.py
@@ -1139,7 +1139,6 @@ def apply_layout(
                 specified will be applied without any expansion. If layout is
                 None, the operator will be expanded to the given number of qubits.
 
-
         Returns:
             A new :class:`.SparsePauliOp` with the provided layout applied
         """
@@ -1159,10 +1158,13 @@ def apply_layout(
                     f"applied to a {n_qubits} qubit operator"
                 )
             n_qubits = num_qubits
-        if layout is not None and any(x >= n_qubits for x in layout):
-            raise QiskitError("Provided layout contains indices outside the number of qubits.")
         if layout is None:
             layout = list(range(self.num_qubits))
+        else:
+            if any(x < 0 or x >= n_qubits for x in layout):
+                raise QiskitError("Provided layout contains indices outside the number of qubits.")
+            if len(set(layout)) != len(layout):
+                raise QiskitError("Provided layout contains duplicate indices.")
         new_op = type(self)("I" * n_qubits)
         return new_op.compose(self, qargs=layout)
 
diff --git a/releasenotes/notes/fix-apply-layout-duplicate-negative-indices-cf5517921fe52706.yaml b/releasenotes/notes/fix-apply-layout-duplicate-negative-indices-cf5517921fe52706.yaml
new file mode 100644
index 000000000000..9fbe0ffd9c79
--- /dev/null
+++ b/releasenotes/notes/fix-apply-layout-duplicate-negative-indices-cf5517921fe52706.yaml
@@ -0,0 +1,6 @@
+---
+fixes:
+  - |
+    Fixed :meth:`.SparsePauliOp.apply_layout` and :meth:`.Pauli.apply_layout`
+    to raise :exc:`.QiskitError` if duplicate indices or negative indices are provided
+    as part of a layout.
diff --git a/test/python/quantum_info/operators/symplectic/test_pauli.py b/test/python/quantum_info/operators/symplectic/test_pauli.py
index 875dd9237810..89324e8212e1 100644
--- a/test/python/quantum_info/operators/symplectic/test_pauli.py
+++ b/test/python/quantum_info/operators/symplectic/test_pauli.py
@@ -606,6 +606,18 @@ def test_apply_layout_null_layout_invalid_num_qubits(self):
         with self.assertRaises(QiskitError):
             op.apply_layout(layout=None, num_qubits=1)
 
+    def test_apply_layout_negative_indices(self):
+        """Test apply_layout with negative indices"""
+        op = Pauli("IZ")
+        with self.assertRaises(QiskitError):
+            op.apply_layout(layout=[-1, 0], num_qubits=3)
+
+    def test_apply_layout_duplicate_indices(self):
+        """Test apply_layout with duplicate indices"""
+        op = Pauli("IZ")
+        with self.assertRaises(QiskitError):
+            op.apply_layout(layout=[0, 0], num_qubits=3)
+
 
 if __name__ == "__main__":
     unittest.main()
diff --git a/test/python/quantum_info/operators/symplectic/test_sparse_pauli_op.py b/test/python/quantum_info/operators/symplectic/test_sparse_pauli_op.py
index 330fd53bc35d..1149ef1f3466 100644
--- a/test/python/quantum_info/operators/symplectic/test_sparse_pauli_op.py
+++ b/test/python/quantum_info/operators/symplectic/test_sparse_pauli_op.py
@@ -1179,6 +1179,18 @@ def test_apply_layout_null_layout_invalid_num_qubits(self):
         with self.assertRaises(QiskitError):
             op.apply_layout(layout=None, num_qubits=1)
 
+    def test_apply_layout_negative_indices(self):
+        """Test apply_layout with negative indices"""
+        op = SparsePauliOp.from_list([("II", 1), ("IZ", 2), ("XI", 3)])
+        with self.assertRaises(QiskitError):
+            op.apply_layout(layout=[-1, 0], num_qubits=3)
+
+    def test_apply_layout_duplicate_indices(self):
+        """Test apply_layout with duplicate indices"""
+        op = SparsePauliOp.from_list([("II", 1), ("IZ", 2), ("XI", 3)])
+        with self.assertRaises(QiskitError):
+            op.apply_layout(layout=[0, 0], num_qubits=3)
+
 
 if __name__ == "__main__":
     unittest.main()