diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
index 9a432e03e9cf4..781b3b2282a87 100644
--- a/doc/source/whatsnew/v3.0.0.rst
+++ b/doc/source/whatsnew/v3.0.0.rst
@@ -222,6 +222,7 @@ Removal of prior version deprecations/changes
 - Disallow automatic casting to object in :class:`Series` logical operations (``&``, ``^``, ``||``) between series with mismatched indexes and dtypes other than ``object`` or ``bool`` (:issue:`52538`)
 - Disallow calling :meth:`Series.replace` or :meth:`DataFrame.replace` without a ``value`` and with non-dict-like ``to_replace`` (:issue:`33302`)
 - Disallow constructing a :class:`arrays.SparseArray` with scalar data (:issue:`53039`)
+- Disallow indexing an :class:`Index` with a boolean indexer of length zero, it now raises ``ValueError`` (:issue:`55820`)
 - Disallow non-standard (``np.ndarray``, :class:`Index`, :class:`ExtensionArray`, or :class:`Series`) to :func:`isin`, :func:`unique`, :func:`factorize` (:issue:`52986`)
 - Disallow passing a pandas type to :meth:`Index.view` (:issue:`55709`)
 - Disallow units other than "s", "ms", "us", "ns" for datetime64 and timedelta64 dtypes in :func:`array` (:issue:`53817`)
diff --git a/pandas/core/indexes/base.py b/pandas/core/indexes/base.py
index d2129c54fabc4..5654111132b5e 100644
--- a/pandas/core/indexes/base.py
+++ b/pandas/core/indexes/base.py
@@ -5033,12 +5033,9 @@ def __getitem__(self, key):
 
             if not isinstance(self.dtype, ExtensionDtype):
                 if len(key) == 0 and len(key) != len(self):
-                    warnings.warn(
-                        "Using a boolean indexer with length 0 on an Index with "
-                        "length greater than 0 is deprecated and will raise in a "
-                        "future version.",
-                        FutureWarning,
-                        stacklevel=find_stack_level(),
+                    raise ValueError(
+                        "The length of the boolean indexer cannot be 0 "
+                        "when the Index has length greater than 0."
                     )
 
         result = getitem(key)
diff --git a/pandas/tests/indexes/test_base.py b/pandas/tests/indexes/test_base.py
index 3a2d04d3ffdc2..301c4794be4ef 100644
--- a/pandas/tests/indexes/test_base.py
+++ b/pandas/tests/indexes/test_base.py
@@ -481,7 +481,7 @@ def test_empty_fancy(self, index, dtype, request, using_infer_string):
 
         assert index[[]].identical(empty_index)
         if dtype == np.bool_:
-            with tm.assert_produces_warning(FutureWarning, match="is deprecated"):
+            with pytest.raises(ValueError, match="length of the boolean indexer"):
                 assert index[empty_arr].identical(empty_index)
         else:
             assert index[empty_arr].identical(empty_index)