diff --git a/src/plugins/intel_gpu/src/graph/graph_optimizer/reorder_inputs.cpp b/src/plugins/intel_gpu/src/graph/graph_optimizer/reorder_inputs.cpp
index 76151622f97da0..426d220116b7ad 100644
--- a/src/plugins/intel_gpu/src/graph/graph_optimizer/reorder_inputs.cpp
+++ b/src/plugins/intel_gpu/src/graph/graph_optimizer/reorder_inputs.cpp
@@ -980,7 +980,7 @@ void reorder_inputs::run(program& p, reorder_factory& rf) {
     // correctly and we need to do it manually
 #ifdef ENABLE_ONEDNN_FOR_GPU
     for (auto& node : p.get_processing_order()) {
-        if (node->is_type<gemm>() && node->get_preferred_impl_type() == impl_types::onednn) {
+        if ((node->is_type<gemm>() || node->is_type<fully_connected>()) && node->get_preferred_impl_type() == impl_types::onednn) {
             for (const auto& fused_prim : node->get_fused_primitives()) {
                 if (fused_prim.is_type<eltwise>() &&
                     one_of(fused_prim.typed_desc<eltwise>()->mode, {eltwise_mode::sum, eltwise_mode::sub, eltwise_mode::prod})) {
diff --git a/src/plugins/intel_gpu/src/graph/program_node.cpp b/src/plugins/intel_gpu/src/graph/program_node.cpp
index 202e1476d71a4c..56ff37a29a9915 100644
--- a/src/plugins/intel_gpu/src/graph/program_node.cpp
+++ b/src/plugins/intel_gpu/src/graph/program_node.cpp
@@ -1549,14 +1549,15 @@ void program_node::create_onednn_primitive_attributes(
                         if (prim->input_size == in_pshape.size()) {
                             ones_to_add = std::max(out_pshape.size(), static_cast<size_t>(rank)) - in_pshape.size();
                         } else {
-                            if (in_pshape.size() > prim->input_size)
-                                ones_to_add = in_pshape.size() - prim->input_size;
+                            if (prim->input_size == 3)
+                                cldnn::onednn::combine_bf_with_first_spatial_dim(in);
+                            ones_to_add = std::max(in_pshape.size(), prim->input_size) - std::min(in_pshape.size(), prim->input_size);
                         }
                         if (ones_to_add > 0) {
                             layout new_layout = in;
                             ov::PartialShape new_input_pshape;
                             auto last = in_pshape.begin() + in_pshape.size();
-                            if (prim->input_size != in_pshape.size())
+                            if (in_pshape.size() > prim->input_size)
                                 last -= ones_to_add;
                             std::vector<ov::Dimension> dims(in_pshape.begin(), last);
                             new_input_pshape = ov::PartialShape(dims);
diff --git a/src/plugins/intel_gpu/tests/unit/fusions/fully_connected_fusion_test.cpp b/src/plugins/intel_gpu/tests/unit/fusions/fully_connected_fusion_test.cpp
index 5e9b5134fb3802..dbc2f9786518ff 100644
--- a/src/plugins/intel_gpu/tests/unit/fusions/fully_connected_fusion_test.cpp
+++ b/src/plugins/intel_gpu/tests/unit/fusions/fully_connected_fusion_test.cpp
@@ -161,13 +161,13 @@ class FullyConnectedFusingTestOneDNN : public BaseFusingTest<fully_connected_tes
 #define CASE_FC_FP32_1 { 1, 3 }, { 1, 4 }, { 4, 3 }, data_types::f32, format::bfyx, data_types::f32, format::oiyx, data_types::f32, format::bfyx
 #define CASE_FC_FP32_2 { 2, 3 }, { 2, 4 }, { 4, 3 }, data_types::f32, format::yxfb, data_types::f32, format::oiyx, data_types::f32, format::bfyx
 #define CASE_FC_FP32_3 { 2, 32 }, { 2, 16 }, { 16, 32 }, data_types::f32, format::bfyx, data_types::i8, format::oiyx, data_types::f32, format::bfyx
-#define CASE_FC_FP32_3D_1 { 5, 3, 3 }, { 5, 3, 5 }, { 5, 3, 1 }, data_types::f32, format::bfyx, data_types::f32, format::os_iyx_osv16, data_types::f32, format::bfyx
-#define CASE_FC_FP32_3D_2 { 2, 1, 1 }, { 2, 1, 32 }, { 32, 1, 1 }, data_types::f32, format::bfyx, data_types::f32, format::os_iyx_osv16, data_types::f32, format::bfyx
-#define CASE_FC_FP32_3D_3 { 2, 32, 32 }, { 2, 32, 16 }, { 16, 32, 1 }, data_types::f32, format::bfyx, data_types::f32, format::os_iyx_osv16, data_types::f32, format::bfyx
+#define CASE_FC_FP32_3D_1 { 5, 3, 3 }, { 5, 3, 5 }, { 5, 3, 1 }, data_types::f32, format::bfyx, data_types::f32, format::oiyx, data_types::f32, format::bfyx
+#define CASE_FC_FP32_3D_2 { 2, 1, 1 }, { 2, 1, 32 }, { 32, 1, 1 }, data_types::f32, format::bfyx, data_types::f32, format::oiyx, data_types::f32, format::bfyx
+#define CASE_FC_FP32_3D_3 { 2, 32, 32 }, { 2, 32, 16 }, { 16, 32, 1 }, data_types::f32, format::bfyx, data_types::f32, format::oiyx, data_types::f32, format::bfyx
 
-#define DYN_CASE_FC_FP32_3D_1 { 5, 3, 3 }, { 5, 3, 5 }, { 5, 3 }, data_types::f32, format::bfyx, data_types::f32, format::os_iyx_osv16, data_types::f32, format::bfyx
-#define DYN_CASE_FC_FP32_3D_2 { 2, 1, 1 }, { 2, 1, 32 }, { 32, 1 }, data_types::f32, format::bfyx, data_types::f32, format::os_iyx_osv16, data_types::f32, format::bfyx
-#define DYN_CASE_FC_FP32_3D_3 { 2, 32, 32 }, { 2, 32, 16 }, { 16, 32 }, data_types::f32, format::bfyx, data_types::f32, format::os_iyx_osv16, data_types::f32, format::bfyx
+#define DYN_CASE_FC_FP32_3D_1 { 5, 3, 3 }, { 5, 3, 5 }, { 5, 3 }, data_types::f32, format::bfyx, data_types::f32, format::oiyx, data_types::f32, format::bfyx
+#define DYN_CASE_FC_FP32_3D_2 { 2, 1, 1 }, { 2, 1, 32 }, { 32, 1 }, data_types::f32, format::bfyx, data_types::f32, format::oiyx, data_types::f32, format::bfyx
+#define DYN_CASE_FC_FP32_3D_3 { 2, 32, 32 }, { 2, 32, 16 }, { 16, 32 }, data_types::f32, format::bfyx, data_types::f32, format::oiyx, data_types::f32, format::bfyx
 
 #define CASE_FC_U8S8_1 { 1, 3 }, { 1, 4 }, { 4, 3 }, data_types::u8, format::bfyx, data_types::i8, format::oiyx, data_types::f32, format::bfyx
 #define CASE_FC_U8S8_2 { 2, 3 }, { 2, 4 }, { 4, 3 }, data_types::u8, format::b_fs_yx_fsv4, data_types::i8, format::oiyx, data_types::f32, format::bfyx