diff --git a/Documentation/config/core.txt b/Documentation/config/core.txt
index 7c640bbf36bb68..cb37bca6d7ac08 100644
--- a/Documentation/config/core.txt
+++ b/Documentation/config/core.txt
@@ -756,6 +756,15 @@ core.gvfs::
 		Bit value 4
 		Normally git write-tree ensures that the objects referenced by the
 		directory exist in the object database. This option disables this check.
+	GVFS_NO_DELETE_OUTSIDE_SPARSECHECKOUT::
+		Bit value 8
+		When marking entries to remove from the index and the working
+		directory this option will take into account what the
+		skip-worktree bit was set to so that if the entry has the
+		skip-worktree bit set it will not be removed from the working
+		directory.  This will allow virtualized working directories to
+		detect the change to HEAD and use the new commit tree to show
+		the files that are in the working directory.
 --
 
 core.sparseCheckout::
diff --git a/gvfs.h b/gvfs.h
index 7bedfaacf6d684..44131625828cfa 100644
--- a/gvfs.h
+++ b/gvfs.h
@@ -13,6 +13,7 @@
  */
 #define GVFS_SKIP_SHA_ON_INDEX                      (1 << 0)
 #define GVFS_MISSING_OK                             (1 << 2)
+#define GVFS_NO_DELETE_OUTSIDE_SPARSECHECKOUT       (1 << 3)
 
 void gvfs_load_config_value(const char *value);
 int gvfs_config_is_set(int mask);
diff --git a/t/t1090-sparse-checkout-scope.sh b/t/t1090-sparse-checkout-scope.sh
index b6298e7e7d8ab1..7af01dc00b75ee 100755
--- a/t/t1090-sparse-checkout-scope.sh
+++ b/t/t1090-sparse-checkout-scope.sh
@@ -107,6 +107,26 @@ test_expect_success 'in partial clone, sparse checkout only fetches needed blobs
 	test_cmp expect actual
 '
 
+test_expect_success 'checkout does not delete items outside the sparse checkout file' '
+	# The "sparse.expectfilesoutsideofpatterns" config will prevent the
+	# SKIP_WORKTREE flag from being dropped on files present on-disk.
+	test_config sparse.expectfilesoutsideofpatterns true &&
+
+	test_config core.gvfs 8 &&
+	git checkout -b outside &&
+	echo "new file1" >d &&
+	git add --sparse d &&
+	git commit -m "branch initial" &&
+	echo "new file1" >e &&
+	git add --sparse e &&
+	git commit -m "skipped worktree" &&
+	git update-index --skip-worktree e &&
+	echo "/d" >.git/info/sparse-checkout &&
+	git checkout HEAD^ &&
+	test_path_is_file d &&
+	test_path_is_file e
+'
+
 test_expect_success MINGW 'no unnecessary opendir() with fscache' '
 	git clone . fscache-test &&
 	(
diff --git a/unpack-trees.c b/unpack-trees.c
index 1cff7ca762374f..7c564ce5566102 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -2,6 +2,7 @@
 
 #include "git-compat-util.h"
 #include "advice.h"
+#include "gvfs.h"
 #include "strvec.h"
 #include "repository.h"
 #include "parse.h"
@@ -2677,6 +2678,27 @@ static int deleted_entry(const struct cache_entry *ce,
 
 	if (!(old->ce_flags & CE_CONFLICTED) && verify_uptodate(old, o))
 		return -1;
+
+	/*
+	 * When marking entries to remove from the index and the working
+	 * directory this option will take into account what the
+	 * skip-worktree bit was set to so that if the entry has the
+	 * skip-worktree bit set it will not be removed from the working
+	 * directory.  This will allow virtualized working directories to
+	 * detect the change to HEAD and use the new commit tree to show
+	 * the files that are in the working directory.
+	 *
+	 * old is the cache_entry that will have the skip-worktree bit set
+	 * which will need to be preserved when the CE_REMOVE entry is added
+	 */
+	if (gvfs_config_is_set(GVFS_NO_DELETE_OUTSIDE_SPARSECHECKOUT) &&
+		old &&
+		old->ce_flags & CE_SKIP_WORKTREE) {
+		add_entry(o, old, CE_REMOVE, 0);
+		invalidate_ce_path(old, o);
+		return 1;
+	}
+
 	add_entry(o, ce, CE_REMOVE, 0);
 	invalidate_ce_path(ce, o);
 	return 1;