diff --git a/src/compiler/precompute_prune.cc b/src/compiler/precompute_prune.cc
index 850a961fc..c3656b640 100644
--- a/src/compiler/precompute_prune.cc
+++ b/src/compiler/precompute_prune.cc
@@ -27,6 +27,25 @@ nnvm::Graph PrecomputePrune(nnvm::Graph src) {
   // number of edges that are not variable
   int non_var_edge = 0;
 
+  auto replace_pruned_entry = [&] (const NodeEntry& e) {
+    if (!entry_var.count(e)) {
+      if (!e.node->is_variable()) {
+        ++non_var_edge;
+      }
+      nnvm::NodePtr var = nnvm::Node::Create();
+      var->attrs.name = e.node->attrs.name;
+      if (e.node->num_outputs() != 1) {
+        var->attrs.name += "_output" + std::to_string(e.index);
+      }
+      entry_var.emplace(e, var);
+      CHECK(!unique_name.count(var->attrs.name));
+      unique_name.insert(var->attrs.name);
+      return nnvm::NodeEntry{var, 0, 0};
+    } else {
+      return nnvm::NodeEntry{entry_var.at(e), 0, 0};
+    }
+  };
+
   DFSVisit(src.outputs, [&](const nnvm::NodePtr& n) {
     bool can_be_pruned = true;
     if (n->is_variable()) {
@@ -47,20 +66,7 @@ nnvm::Graph PrecomputePrune(nnvm::Graph src) {
       // scan again to find edge nodes, skip variables
       for (auto& e : n->inputs) {
         if (pruned.count(e.node.get())) {
-          if (!entry_var.count(e)) {
-            if (!e.node->is_variable()) {
-              ++non_var_edge;
-            }
-            nnvm::NodePtr var = nnvm::Node::Create();
-            var->attrs.name = e.node->attrs.name;
-            if (e.node->num_outputs() != 1) {
-              var->attrs.name += "_output" + std::to_string(e.index);
-            }
-            entry_var.emplace(e, var);
-            CHECK(!unique_name.count(var->attrs.name));
-            unique_name.insert(var->attrs.name);
-          }
-          e = nnvm::NodeEntry{entry_var.at(e), 0, 0};
+          e = replace_pruned_entry(e);
         }
       }
     }
@@ -71,6 +77,12 @@ nnvm::Graph PrecomputePrune(nnvm::Graph src) {
     return src;
   }
 
+  for (auto& e : src.outputs) {
+    if (pruned.count(e.node.get())) {
+      e = replace_pruned_entry(e);
+    }
+  }
+
   nnvm::Graph pre_graph;
   pre_graph.outputs.reserve(entry_var.size());
   std::vector<std::string> output_names;