diff --git a/doc/source/whatsnew/v0.25.0.rst b/doc/source/whatsnew/v0.25.0.rst
index 284943cf49070..ab2f8d66c37da 100644
--- a/doc/source/whatsnew/v0.25.0.rst
+++ b/doc/source/whatsnew/v0.25.0.rst
@@ -215,6 +215,7 @@ I/O
 - Bug in :func:`read_json` for ``orient='table'`` and float index, as it infers index dtype by default, which is not applicable because index dtype is already defined in the JSON schema (:issue:`25433`)
 - Bug in :func:`read_json` for ``orient='table'`` and string of float column names, as it makes a column name type conversion to Timestamp, which is not applicable because column names are already defined in the JSON schema (:issue:`25435`)
 - :meth:`DataFrame.to_html` now raises ``TypeError`` when using an invalid type for the ``classes`` parameter instead of ``AsseertionError`` (:issue:`25608`)
+- Bug in :meth:`DataFrame.to_string` and :meth:`DataFrame.to_latex` that would lead to incorrect output when the ``header`` keyword is used (:issue:`16718`)
 -
 -
 
diff --git a/pandas/io/formats/format.py b/pandas/io/formats/format.py
index f68ef2cc39006..91e5edc8de9f4 100644
--- a/pandas/io/formats/format.py
+++ b/pandas/io/formats/format.py
@@ -528,6 +528,10 @@ def _to_str_columns(self):
             else:
                 str_columns = self._get_formatted_column_labels(frame)
 
+            if self.show_row_idx_names:
+                for x in str_columns:
+                    x.append('')
+
             stringified = []
             for i, c in enumerate(frame):
                 cheader = str_columns[i]
@@ -770,11 +774,6 @@ def space_format(x, y):
                             need_leadsp[x] else x]
                            for i, (col, x) in enumerate(zip(columns,
                                                             fmt_columns))]
-
-        if self.show_row_idx_names:
-            for x in str_columns:
-                x.append('')
-
         # self.str_columns = str_columns
         return str_columns
 
diff --git a/pandas/tests/io/formats/test_format.py b/pandas/tests/io/formats/test_format.py
index b0cf5a2f17609..43bb382ea3f20 100644
--- a/pandas/tests/io/formats/test_format.py
+++ b/pandas/tests/io/formats/test_format.py
@@ -2380,6 +2380,14 @@ def test_to_string_header(self):
         exp = '0    0\n    ..\n9    9'
         assert res == exp
 
+    def test_to_string_multindex_header(self):
+        # GH 16718
+        df = (pd.DataFrame({'a': [0], 'b': [1], 'c': [2], 'd': [3]})
+              .set_index(['a', 'b']))
+        res = df.to_string(header=['r1', 'r2'])
+        exp = '    r1 r2\na b      \n0 1  2  3'
+        assert res == exp
+
 
 def _three_digit_exp():
     return '{x:.4g}'.format(x=1.7e8) == '1.7e+008'
diff --git a/pandas/tests/io/formats/test_to_latex.py b/pandas/tests/io/formats/test_to_latex.py
index 1653e474aa7b0..4bec3bca1820b 100644
--- a/pandas/tests/io/formats/test_to_latex.py
+++ b/pandas/tests/io/formats/test_to_latex.py
@@ -735,3 +735,19 @@ def test_to_latex_float_format_no_fixed_width(self):
 \end{tabular}
 """
         assert df.to_latex(float_format='%.0f') == expected
+
+    def test_to_latex_multindex_header(self):
+        # GH 16718
+        df = (pd.DataFrame({'a': [0], 'b': [1], 'c': [2], 'd': [3]})
+              .set_index(['a', 'b']))
+        observed = df.to_latex(header=['r1', 'r2'])
+        expected = r"""\begin{tabular}{llrr}
+\toprule
+  &   & r1 & r2 \\
+a & b &    &    \\
+\midrule
+0 & 1 &  2 &  3 \\
+\bottomrule
+\end{tabular}
+"""
+        assert observed == expected