diff --git a/pkg/vm/ref_counter_test.go b/pkg/vm/ref_counter_test.go
index 2c2b3752d9..4e57ae0f6a 100644
--- a/pkg/vm/ref_counter_test.go
+++ b/pkg/vm/ref_counter_test.go
@@ -3,6 +3,7 @@ package vm
 import (
 	"testing"
 
+	"github.com/nspcc-dev/neo-go/pkg/vm/opcode"
 	"github.com/nspcc-dev/neo-go/pkg/vm/stackitem"
 	"github.com/stretchr/testify/require"
 )
@@ -46,6 +47,19 @@ func TestRefCounter_Add(t *testing.T) {
 	require.Equal(t, 2, int(*r))
 }
 
+func TestRefCounterPopItem(t *testing.T) {
+	prog := makeProgram(opcode.POPITEM)
+	v := load(prog)
+	v.estack.PushVal(stackitem.NewArray([]stackitem.Item{stackitem.Make(42)}))
+	require.Equal(t, 2, int(v.refs))
+	runVM(t, v)
+	require.Equal(t, 1, v.estack.Len())
+	require.Equal(t, 1, int(v.refs))
+	_ = v.estack.Pop()
+	require.Equal(t, 0, v.estack.Len())
+	require.Equal(t, 0, int(v.refs))
+}
+
 func BenchmarkRefCounter_Add(b *testing.B) {
 	a := stackitem.NewArray(nil)
 	rc := newRefCounter()
diff --git a/pkg/vm/vm.go b/pkg/vm/vm.go
index 2569fb9055..8c98192c39 100644
--- a/pkg/vm/vm.go
+++ b/pkg/vm/vm.go
@@ -1459,7 +1459,6 @@ func (v *VM) execute(ctx *Context, op opcode.Opcode, parameter []byte) (err erro
 		case *stackitem.Struct:
 			item.Remove(index)
 		}
-		v.refs.Remove(elem)
 
 	case opcode.SIZE:
 		elem := v.estack.Pop()