diff --git a/.github/CHANGELOG.md b/.github/CHANGELOG.md
index 348164054c..13ee775fb2 100644
--- a/.github/CHANGELOG.md
+++ b/.github/CHANGELOG.md
@@ -46,6 +46,9 @@
 
 ### Improvements
 
+* Add joint check for the N-controlled wires support in `lightning.qubit`.
+  [(#949)](https://github.com/PennyLaneAI/pennylane-lightning/pull/949)
+
 * Optimize the cartesian product to reduce the amount of memory necessary to set the StatePrep with LightningTensor. 
   [(#943)](https://github.com/PennyLaneAI/pennylane-lightning/pull/943)
 
diff --git a/pennylane_lightning/core/_version.py b/pennylane_lightning/core/_version.py
index 37f7ba1bbf..de59ceba06 100644
--- a/pennylane_lightning/core/_version.py
+++ b/pennylane_lightning/core/_version.py
@@ -16,4 +16,4 @@
    Version number (major.minor.patch[-label])
 """
 
-__version__ = "0.39.0-dev46"
+__version__ = "0.39.0-dev47"
diff --git a/pennylane_lightning/core/src/simulators/lightning_qubit/StateVectorLQubit.hpp b/pennylane_lightning/core/src/simulators/lightning_qubit/StateVectorLQubit.hpp
index 78521ebe8b..cf0ed2f632 100644
--- a/pennylane_lightning/core/src/simulators/lightning_qubit/StateVectorLQubit.hpp
+++ b/pennylane_lightning/core/src/simulators/lightning_qubit/StateVectorLQubit.hpp
@@ -369,6 +369,10 @@ class StateVectorLQubit : public StateVectorBase<PrecisionT, Derived> {
                         const std::vector<std::size_t> &wires,
                         bool inverse = false,
                         const std::vector<PrecisionT> &params = {}) {
+        PL_ABORT_IF_NOT(
+            areVecsDisjoint<std::size_t>(controlled_wires, wires),
+            "`controlled_wires` and `target wires` must be disjoint.");
+
         PL_ABORT_IF_NOT(controlled_wires.size() == controlled_values.size(),
                         "`controlled_wires` must have the same size as "
                         "`controlled_values`.");
@@ -420,6 +424,10 @@ class StateVectorLQubit : public StateVectorBase<PrecisionT, Derived> {
                         const std::vector<std::size_t> &wires, bool inverse,
                         const std::vector<PrecisionT> &params,
                         const std::vector<ComplexT, Alloc> &matrix) {
+        PL_ABORT_IF_NOT(
+            areVecsDisjoint<std::size_t>(controlled_wires, wires),
+            "`controlled_wires` and `target wires` must be disjoint.");
+
         PL_ABORT_IF_NOT(controlled_wires.size() == controlled_values.size(),
                         "`controlled_wires` must have the same size as "
                         "`controlled_values`.");
@@ -569,6 +577,9 @@ class StateVectorLQubit : public StateVectorBase<PrecisionT, Derived> {
                           const std::vector<bool> &controlled_values,
                           const std::vector<std::size_t> &wires,
                           bool inverse = false) {
+        PL_ABORT_IF_NOT(
+            areVecsDisjoint<std::size_t>(controlled_wires, wires),
+            "`controlled_wires` and `target wires` must be disjoint.");
         applyControlledMatrix(matrix.data(), controlled_wires,
                               controlled_values, wires, inverse);
     }
diff --git a/pennylane_lightning/core/src/simulators/lightning_qubit/gates/tests/Test_GateImplementations_Nonparam.cpp b/pennylane_lightning/core/src/simulators/lightning_qubit/gates/tests/Test_GateImplementations_Nonparam.cpp
index 305d161f2e..afd371f7aa 100644
--- a/pennylane_lightning/core/src/simulators/lightning_qubit/gates/tests/Test_GateImplementations_Nonparam.cpp
+++ b/pennylane_lightning/core/src/simulators/lightning_qubit/gates/tests/Test_GateImplementations_Nonparam.cpp
@@ -674,6 +674,14 @@ TEMPLATE_TEST_CASE("StateVectorLQubitManaged::applyOperation non-param "
                     << "controls = {" << control << "} "
                     << ", wires = {" << wire << "} - "
                     << PrecisionToName<PrecisionT>::value) {
+        if (control == wire) {
+            REQUIRE_THROWS_AS(
+                sv0.applyOperation("PauliX", std::vector<std::size_t>{control},
+                                   std::vector<bool>{true},
+                                   std::vector<std::size_t>{wire}),
+                LightningException);
+        }
+
         if (control != wire) {
             auto st0 = createRandomStateVectorData<PrecisionT>(re, num_qubits);
             sv0.updateData(st0);
@@ -687,7 +695,7 @@ TEMPLATE_TEST_CASE("StateVectorLQubitManaged::applyOperation non-param "
                     approx(sv1.getDataVector()).margin(margin));
         }
 
-        if (control != 0 && wire != 0) {
+        if (control != 0 && wire != 0 && control != wire) {
             sv0.applyOperation("Toffoli", {0, control, wire});
             sv1.applyOperation("PauliX", std::vector<std::size_t>{0, control},
                                std::vector<bool>{true, true},
@@ -760,6 +768,15 @@ TEMPLATE_TEST_CASE("StateVectorLQubitManaged::applyOperation non-param "
             REQUIRE(sv0.getDataVector() ==
                     approx(sv1.getDataVector()).margin(margin));
         }
+
+        if (control == wire) {
+            const auto matrix = getHadamard<std::complex, PrecisionT>();
+            REQUIRE_THROWS_AS(sv0.applyControlledMatrix(
+                                  matrix, std::vector<std::size_t>{control},
+                                  std::vector<bool>{true},
+                                  std::vector<std::size_t>{wire}),
+                              LightningException);
+        }
     }
     DYNAMIC_SECTION("N-controlled S - "
                     << "controls = {" << control << "} "
diff --git a/pennylane_lightning/core/src/utils/Util.hpp b/pennylane_lightning/core/src/utils/Util.hpp
index 5478cdbdcb..6f512ac40d 100644
--- a/pennylane_lightning/core/src/utils/Util.hpp
+++ b/pennylane_lightning/core/src/utils/Util.hpp
@@ -574,4 +574,22 @@ std::vector<T1> cast_vector(const std::vector<T0> &vec) {
     return result;
 }
 
+/**
+ * @brief Check if two vectors are disjoint.
+ * @tparam T Data type.
+ * @param v1 First vector.
+ * @param v2 Second vector.
+ *
+ * @return bool True if the vectors are disjoint, false otherwise.
+ */
+template <typename T = std::size_t>
+bool areVecsDisjoint(const std::vector<T> &v1, const std::vector<T> &v2) {
+    std::set<T> s0(v1.begin(), v1.end());
+    for (const auto &element : v2) {
+        if (s0.find(element) != s0.end()) {
+            return false;
+        }
+    }
+    return true;
+}
 } // namespace Pennylane::Util
diff --git a/pennylane_lightning/core/src/utils/tests/Test_Util.cpp b/pennylane_lightning/core/src/utils/tests/Test_Util.cpp
index 4f52318fdd..2ba66c779f 100644
--- a/pennylane_lightning/core/src/utils/tests/Test_Util.cpp
+++ b/pennylane_lightning/core/src/utils/tests/Test_Util.cpp
@@ -217,3 +217,19 @@ TEMPLATE_TEST_CASE("Util::kronProd", "[Util][LinearAlgebra]", float, double) {
         CHECK(vec == expected);
     }
 }
+
+TEST_CASE("Util::areVecsDisjoint", "[Util][LinearAlgebra]") {
+    SECTION("Test for disjoint vectors") {
+        std::vector<std::size_t> vec0{0, 1, 2};
+        std::vector<std::size_t> vec1{3, 4, 5};
+
+        REQUIRE(areVecsDisjoint(vec0, vec1) == true);
+    }
+
+    SECTION("Test for joint vectors") {
+        std::vector<std::size_t> vec0{0, 1, 2};
+        std::vector<std::size_t> vec1{2, 4, 5};
+
+        REQUIRE(areVecsDisjoint(vec0, vec1) == false);
+    }
+}