diff --git a/libio/fileops.c b/libio/fileops.c
index 12b440b09d..42e695265d 100644
--- a/libio/fileops.c
+++ b/libio/fileops.c
@@ -800,6 +800,11 @@ _IO_new_file_sync (FILE *fp)
   if (fp->_IO_write_ptr > fp->_IO_write_base)
     if (_IO_do_flush(fp)) return EOF;
   delta = fp->_IO_read_ptr - fp->_IO_read_end;
+  if (_IO_in_backup (fp))
+    {
+      _IO_switch_to_main_get_area (fp);
+      delta += fp->_IO_read_ptr - fp->_IO_read_end;
+    }
   if (delta != 0)
     {
       off64_t new_pos = _IO_SYSSEEK (fp, delta, 1);
diff --git a/stdio-common/Makefile b/stdio-common/Makefile
index 1e7bca641e..4a3810cdf2 100644
--- a/stdio-common/Makefile
+++ b/stdio-common/Makefile
@@ -305,6 +305,7 @@ tests := \
   tst-swscanf \
   tst-tmpnam \
   tst-ungetc \
+  tst-ungetc-fflush \
   tst-ungetc-leak \
   tst-ungetc-nomem \
   tst-unlockedio \
diff --git a/stdio-common/tst-ungetc-fflush.c b/stdio-common/tst-ungetc-fflush.c
new file mode 100644
index 0000000000..a86d1fdb7f
--- /dev/null
+++ b/stdio-common/tst-ungetc-fflush.c
@@ -0,0 +1,64 @@
+/* Test flushing input file after ungetc (bug 5994).
+   Copyright (C) 2025 Free Software Foundation, Inc.
+   This file is part of the GNU C Library.
+
+   The GNU C Library is free software; you can redistribute it and/or
+   modify it under the terms of the GNU Lesser General Public
+   License as published by the Free Software Foundation; either
+   version 2.1 of the License, or (at your option) any later version.
+
+   The GNU C Library is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+   Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public
+   License along with the GNU C Library; if not, see
+   <https://www.gnu.org/licenses/>.  */
+
+#include <stdio.h>
+
+#include <support/check.h>
+#include <support/temp_file.h>
+#include <support/xstdio.h>
+#include <support/xunistd.h>
+
+int
+do_test (void)
+{
+  char *filename = NULL;
+  int fd = create_temp_file ("tst-ungetc-fflush", &filename);
+  TEST_VERIFY_EXIT (fd != -1);
+  xclose (fd);
+
+  /* Test as in bug 5994.  */
+  FILE *fp = xfopen (filename, "w");
+  TEST_VERIFY_EXIT (fputs ("#include", fp) >= 0);
+  xfclose (fp);
+  fp = xfopen (filename, "r");
+  TEST_COMPARE (fgetc (fp), '#');
+  TEST_COMPARE (fgetc (fp), 'i');
+  TEST_COMPARE (ungetc ('@', fp), '@');
+  TEST_COMPARE (fflush (fp), 0);
+  TEST_COMPARE (lseek (fileno (fp), 0, SEEK_CUR), 1);
+  TEST_COMPARE (fgetc (fp), 'i');
+  TEST_COMPARE (fgetc (fp), 'n');
+  xfclose (fp);
+
+  /* Test as in bug 12799 (duplicate of 5994).  */
+  fp = xfopen (filename, "w+");
+  TEST_VERIFY_EXIT (fputs ("hello world", fp) >= 0);
+  rewind (fp);
+  TEST_VERIFY (fileno (fp) >= 0);
+  char buffer[10];
+  TEST_COMPARE (fread (buffer, 1, 5, fp), 5);
+  TEST_COMPARE (fgetc (fp), ' ');
+  TEST_COMPARE (ungetc ('@', fp), '@');
+  TEST_COMPARE (fflush (fp), 0);
+  TEST_COMPARE (fgetc (fp), ' ');
+  xfclose (fp);
+
+  return 0;
+}
+
+#include <support/test-driver.c>