diff --git a/include/mxnet/ndarray.h b/include/mxnet/ndarray.h
index 2eed979387f3..c55cb01b4688 100644
--- a/include/mxnet/ndarray.h
+++ b/include/mxnet/ndarray.h
@@ -909,6 +909,9 @@ class NDArray {
       // aux_handles always reflect the correct number of aux data
       for (size_t i = 0; i < aux_shapes.size(); i++) {
         CheckAndAllocAuxData(i, aux_shapes[i]);
+        // this line is needed in case when aux_shapes[i].Size() = 0
+        // aux_handles[i] will not be updated and take only default value.
+        aux_handles[i].ctx = ctx;
       }
       if (!delay_alloc) {
         CheckAndAllocData(storage_shape, dtype);
@@ -983,8 +986,8 @@ class NDArray {
 #endif
         delay_alloc = false;
       } else if (shandle.size < dbytes) {
-        // free storage
-        Storage::Get()->Free(shandle);
+        // free storage if necessary and alloc again
+        if (shandle.size > 0) Storage::Get()->Free(shandle);
         // init storage
         shandle = Storage::Get()->Alloc(dbytes, shandle.ctx);
 #if MXNET_USE_MKLDNN == 1
@@ -1049,14 +1052,12 @@ class NDArray {
         << "storage type cannot be kDefaultStorage in CheckAndAllocAuxData";
       if (aux_handles.size() <= i) {
         aux_handles.resize(i + 1);
-        // set context for the newly created aux handle
-        aux_handles[i].ctx = ctx;
       }
       size_t aux_bytes = shape.Size() * mshadow::mshadow_sizeof(aux_types[i]);
       if (aux_handles[i].size < aux_bytes) {
-        // free storage
-        Storage::Get()->Free(aux_handles[i]);
-        // init storage
+        // free storage if necessary and alloc again
+        if (aux_handles[i].size > 0) Storage::Get()->Free(aux_handles[i]);
+        // init aux storage
         aux_handles[i] = Storage::Get()->Alloc(aux_bytes, ctx);
       }
       // init shape
diff --git a/src/ndarray/ndarray.cc b/src/ndarray/ndarray.cc
index 377bef072b03..367712755483 100644
--- a/src/ndarray/ndarray.cc
+++ b/src/ndarray/ndarray.cc
@@ -121,9 +121,9 @@ NDArray::Chunk::~Chunk() {
         CHECK_EQ(mem.mem->GetDataHandle(), mem.h.dptr);
       }
 #endif
-      Storage::Get()->Free(mem.h);
+      if (mem.h.size > 0) Storage::Get()->Free(mem.h);
       for (const auto& aux : mem.aux_h) {
-        Storage::Get()->Free(aux);
+        if (aux.size > 0) Storage::Get()->Free(aux);
       }
     }
   }, shandle.ctx, var);
@@ -134,8 +134,8 @@ void NDArray::Chunk::CheckAndAllocData(const mxnet::TShape &shape, int dtype) {
       << "data is expected to be allocated after aux_data";
   auto dbytes = shape.Size() * mshadow::mshadow_sizeof(dtype);
   if (shandle.size < dbytes) {
-    // free storage
-    Storage::Get()->Free(shandle);
+    // free storage if necessary and alloc again
+    if (shandle.size > 0) Storage::Get()->Free(shandle);
     // init storage
     shandle = Storage::Get()->Alloc(dbytes, ctx);
 #if MXNET_USE_MKLDNN == 1
diff --git a/src/storage/pooled_storage_manager.h b/src/storage/pooled_storage_manager.h
index 7c4b070afdd2..c407a9f00cb6 100644
--- a/src/storage/pooled_storage_manager.h
+++ b/src/storage/pooled_storage_manager.h
@@ -155,10 +155,6 @@ void GPUPooledStorageManager::Alloc(Storage::Handle* handle) {
 }
 
 void GPUPooledStorageManager::Free(Storage::Handle handle) {
-  // Do nothing if dptr is nullptr. Otherwise, nullptr may be reused
-  // which can cause illegal memory access error.
-  if (handle.dptr == nullptr) return;
-
   std::lock_guard<std::mutex> lock(Storage::Get()->GetMutex(Context::kGPU));
   size_t size = RoundAllocSize(handle.size);
   auto&& reuse_pool = memory_pool_[size];
@@ -316,10 +312,6 @@ void GPUPooledRoundedStorageManager::Alloc(Storage::Handle* handle) {
 }
 
 void GPUPooledRoundedStorageManager::Free(Storage::Handle handle) {
-  // Do nothing if dptr is nullptr. Otherwise, nullptr may be reused
-  // which can cause illegal memory access error.
-  if (handle.dptr == nullptr) return;
-
   std::lock_guard<std::mutex> lock(Storage::Get()->GetMutex(Context::kGPU));
   int bucket = get_bucket(handle.size);
   auto&& reuse_pool = memory_pool_[bucket];