diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
index ee9d18d0c7ce2..eb061f16b5152 100644
--- a/doc/source/whatsnew/v3.0.0.rst
+++ b/doc/source/whatsnew/v3.0.0.rst
@@ -621,6 +621,7 @@ Reshaping
 ^^^^^^^^^
 - Bug in :func:`qcut` where values at the quantile boundaries could be incorrectly assigned (:issue:`59355`)
 - Bug in :meth:`DataFrame.join` inconsistently setting result index name (:issue:`55815`)
+- Bug in :meth:`DataFrame.merge` where merging on a column containing only ``NaN`` values resulted in an out-of-bounds array access (:issue:`59421`)
 - Bug in :meth:`DataFrame.unstack` producing incorrect results when ``sort=False`` (:issue:`54987`, :issue:`55516`)
 - Bug in :meth:`DataFrame.unstack` producing incorrect results when manipulating empty :class:`DataFrame` with an :class:`ExtentionDtype` (:issue:`59123`)
 
diff --git a/pandas/core/algorithms.py b/pandas/core/algorithms.py
index 948836bf6a51d..56f8adda93251 100644
--- a/pandas/core/algorithms.py
+++ b/pandas/core/algorithms.py
@@ -1529,9 +1529,7 @@ def safe_sort(
         order2 = sorter.argsort()
         if verify:
             mask = (codes < -len(values)) | (codes >= len(values))
-            codes[mask] = 0
-        else:
-            mask = None
+            codes[mask] = -1
         new_codes = take_nd(order2, codes, fill_value=-1)
     else:
         reverse_indexer = np.empty(len(sorter), dtype=int)
@@ -1540,14 +1538,6 @@ def safe_sort(
         # may deal with them here without performance loss using `mode='wrap'`
         new_codes = reverse_indexer.take(codes, mode="wrap")
 
-        if use_na_sentinel:
-            mask = codes == -1
-            if verify:
-                mask = mask | (codes < -len(values)) | (codes >= len(values))
-
-    if use_na_sentinel and mask is not None:
-        np.putmask(new_codes, mask, -1)
-
     return ordered, ensure_platform_int(new_codes)
 
 
diff --git a/pandas/tests/reshape/merge/test_merge.py b/pandas/tests/reshape/merge/test_merge.py
index ad704d87a491b..cbee85f4aede9 100644
--- a/pandas/tests/reshape/merge/test_merge.py
+++ b/pandas/tests/reshape/merge/test_merge.py
@@ -2998,3 +2998,15 @@ def test_merge_datetime_and_timedelta(how):
     )
     with pytest.raises(ValueError, match=re.escape(msg)):
         right.merge(left, on="key", how=how)
+
+
+def test_merge_on_all_nan_column():
+    # GH#59421
+    left = DataFrame({"x": [1, 2, 3], "y": [np.nan, np.nan, np.nan], "z": [4, 5, 6]})
+    right = DataFrame({"x": [1, 2, 3], "y": [np.nan, np.nan, np.nan], "zz": [4, 5, 6]})
+    result = left.merge(right, on=["x", "y"], how="outer")
+    # Should not trigger array bounds eerror with bounds checking or asan enabled.
+    expected = DataFrame(
+        {"x": [1, 2, 3], "y": [np.nan, np.nan, np.nan], "z": [4, 5, 6], "zz": [4, 5, 6]}
+    )
+    tm.assert_frame_equal(result, expected)
diff --git a/pandas/tests/test_sorting.py b/pandas/tests/test_sorting.py
index 2a225bda953cf..869d41efa6c28 100644
--- a/pandas/tests/test_sorting.py
+++ b/pandas/tests/test_sorting.py
@@ -408,6 +408,13 @@ def test_codes_out_of_bound(self):
         tm.assert_numpy_array_equal(result, expected)
         tm.assert_numpy_array_equal(result_codes, expected_codes)
 
+    @pytest.mark.parametrize("codes", [[-1, -1], [2, -1], [2, 2]])
+    def test_codes_empty_array_out_of_bound(self, codes):
+        empty_values = np.array([])
+        expected_codes = -np.ones_like(codes, dtype=np.intp)
+        _, result_codes = safe_sort(empty_values, codes)
+        tm.assert_numpy_array_equal(result_codes, expected_codes)
+
     def test_mixed_integer(self):
         values = np.array(["b", 1, 0, "a", 0, "b"], dtype=object)
         result = safe_sort(values)