diff --git a/src/plugins/intel_gpu/src/graph/impls/ocl/non_zero.cpp b/src/plugins/intel_gpu/src/graph/impls/ocl/non_zero.cpp
index 22753be0a71a43..c8f0a5cbae10c0 100644
--- a/src/plugins/intel_gpu/src/graph/impls/ocl/non_zero.cpp
+++ b/src/plugins/intel_gpu/src/graph/impls/ocl/non_zero.cpp
@@ -34,6 +34,15 @@ struct count_nonzero_impl : typed_primitive_impl_ocl<count_nonzero> {
         }
     }
 
+    event::ptr execute_impl(const std::vector<event::ptr>& events, count_nonzero_inst& instance) override {
+        if (instance.get_impl_params()->input_layouts[0].count() == 0) {
+            // set count of non-zero elements to 0 in case if input tensor is empty to have correct memory alloc for gather_nonzero
+            return instance.output_memory(0).fill(instance.get_network().get_stream(), 0);
+        } else {
+            return parent::execute_impl(events, instance);
+        }
+    }
+
     static kernel_params_t get_kernel_params(const kernel_impl_params& impl_param, bool is_shape_agnostic = false) {
         return get_default_params<kernel_selector::count_nonzero_params>(impl_param, is_shape_agnostic);
     }
diff --git a/src/plugins/intel_gpu/tests/unit/test_cases/non_zero_gpu_test.cpp b/src/plugins/intel_gpu/tests/unit/test_cases/non_zero_gpu_test.cpp
index a4543197bcbd0a..37a1ba8b982414 100644
--- a/src/plugins/intel_gpu/tests/unit/test_cases/non_zero_gpu_test.cpp
+++ b/src/plugins/intel_gpu/tests/unit/test_cases/non_zero_gpu_test.cpp
@@ -533,3 +533,42 @@ TEST(non_zero_gpu, const_input) {
         ASSERT_FLOAT_EQ(output_ptr[i], out_data[i]);
     }
 }
+
+TEST(non_zero_gpu, empty_input) {
+    auto& engine = get_test_engine();
+    auto in_layout = layout{ov::PartialShape{1, -1}, data_types::f32, format::bfyx};
+    auto in_data_layout = layout{ov::PartialShape{1, 0}, data_types::f32, format::bfyx};
+    auto input_data_mem = engine.allocate_memory(in_data_layout);
+
+    topology topology;
+    topology.add(input_layout("input", in_layout));
+    topology.add(count_nonzero("count_nonzero", input_info("input")));
+    topology.add(gather_nonzero("gather_nonzero", input_info("input"), input_info("count_nonzero")));
+
+    ExecutionConfig config = get_test_default_config(engine);
+    config.set_property(ov::intel_gpu::optimize_data(true));
+    config.set_property(ov::intel_gpu::allow_new_shape_infer(true));
+    network net(engine, topology, config);
+
+    net.set_input_data("input", input_data_mem);
+
+    auto count_nonzero_inst = net.get_primitive("count_nonzero");
+
+    // Put some value into out buffer to ensure that it's non empty
+    // That is needed to ensure that implementation correctly handles the cases when input tensor is empty and set count non zero to 0
+    count_nonzero_inst->output_memory(0).fill(engine.get_service_stream(), 1);
+    engine.get_service_stream().finish();
+
+    auto count_nonzero_impl = count_nonzero_inst->get_impl();
+    ASSERT_TRUE(count_nonzero_impl != nullptr);
+
+    auto gather_nonzero_inst = net.get_primitive("gather_nonzero");
+    auto gather_nonzero_impl = gather_nonzero_inst->get_impl();
+    ASSERT_TRUE(gather_nonzero_impl != nullptr);
+    ASSERT_TRUE(gather_nonzero_impl->is_dynamic());
+
+    auto outputs = net.execute();
+
+    auto output = outputs.at("gather_nonzero").get_memory();
+    ASSERT_EQ(output, nullptr);
+}