diff --git a/CHANGES.rst b/CHANGES.rst
index 1d04bc27010..4b920ca3911 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -20,5 +20,11 @@ Bugs fixed
   :confval:`intersphinx_cache_limit`.
   Patch by Shengyu Zhang.
 
+* #12730: The ``UnreferencedFootnotesDetector`` transform has been improved
+  to more consistently detect unreferenced footnotes.
+  Note, the priority of the transform has been changed from 200 to 622,
+  so that it now runs after the docutils ``Footnotes`` resolution transform.
+  Patch by Chris Sewell.
+
 Testing
 -------
diff --git a/sphinx/transforms/__init__.py b/sphinx/transforms/__init__.py
index 7ccef6aacaa..5fe133137fd 100644
--- a/sphinx/transforms/__init__.py
+++ b/sphinx/transforms/__init__.py
@@ -9,6 +9,7 @@
 from docutils import nodes
 from docutils.transforms import Transform, Transformer
 from docutils.transforms.parts import ContentsFilter
+from docutils.transforms.references import Footnotes
 from docutils.transforms.universal import SmartQuotes
 from docutils.utils import normalize_language_tag
 from docutils.utils.smartquotes import smartchars
@@ -294,23 +295,40 @@ class UnreferencedFootnotesDetector(SphinxTransform):
     Detect unreferenced footnotes and emit warnings
     """
 
-    default_priority = 200
+    default_priority = Footnotes.default_priority + 2
 
     def apply(self, **kwargs: Any) -> None:
         for node in self.document.footnotes:
-            if node['names'] == []:
-                # footnote having duplicated number.  It is already warned at parser.
-                pass
-            elif node['names'][0] not in self.document.footnote_refs:
-                logger.warning(__('Footnote [%s] is not referenced.'), node['names'][0],
-                               type='ref', subtype='footnote',
-                               location=node)
-
+            # note we do not warn on duplicate footnotes here
+            # (i.e. where the name has been moved to dupnames)
+            # since this is already reported by docutils
+            if not node['backrefs'] and node["names"]:
+                logger.warning(
+                    __('Footnote [%s] is not referenced.'),
+                    node['names'][0] if node['names'] else node['dupnames'][0],
+                    type='ref',
+                    subtype='footnote',
+                    location=node
+                )
+        for node in self.document.symbol_footnotes:
+            if not node['backrefs']:
+                logger.warning(
+                    __('Footnote [*] is not referenced.'),
+                    type='ref',
+                    subtype='footnote',
+                    location=node
+                )
         for node in self.document.autofootnotes:
-            if not any(ref['auto'] == node['auto'] for ref in self.document.autofootnote_refs):
-                logger.warning(__('Footnote [#] is not referenced.'),
-                               type='ref', subtype='footnote',
-                               location=node)
+            # note we do not warn on duplicate footnotes here
+            # (i.e. where the name has been moved to dupnames)
+            # since this is already reported by docutils
+            if not node['backrefs'] and node["names"]:
+                logger.warning(
+                    __('Footnote [#] is not referenced.'),
+                    type='ref',
+                    subtype='footnote',
+                    location=node
+                )
 
 
 class DoctestTransform(SphinxTransform):
diff --git a/tests/test_transforms/test_unreferenced_footnotes.py b/tests/test_transforms/test_unreferenced_footnotes.py
new file mode 100644
index 00000000000..938adcb7fc6
--- /dev/null
+++ b/tests/test_transforms/test_unreferenced_footnotes.py
@@ -0,0 +1,39 @@
+"""Test the ``UnreferencedFootnotesDetector`` transform."""
+
+from pathlib import Path
+
+from sphinx.testing.util import SphinxTestApp
+from sphinx.util.console import strip_colors
+
+
+def test_warnings(make_app: type[SphinxTestApp], tmp_path: Path) -> None:
+    """Test that warnings are emitted for unreferenced footnotes."""
+    tmp_path.joinpath("conf.py").touch()
+    tmp_path.joinpath("index.rst").write_text(
+        """
+Title
+=====
+[1]_ [#label2]_
+
+.. [1] This is a normal footnote.
+.. [2] This is a normal footnote.
+.. [2] This is a normal footnote.
+.. [3] This is a normal footnote.
+.. [*] This is a symbol footnote.
+.. [#] This is an auto-numbered footnote.
+.. [#label1] This is an auto-numbered footnote with a label.
+.. [#label1] This is an auto-numbered footnote with a label.
+.. [#label2] This is an auto-numbered footnote with a label.
+        """, encoding="utf8"
+    )
+    app = make_app(srcdir=tmp_path)
+    app.build()
+    warnings = strip_colors(app.warning.getvalue()).replace(str(tmp_path / "index.rst"), "source/index.rst")
+    print(warnings)
+    assert warnings.strip() == """
+source/index.rst:8: WARNING: Duplicate explicit target name: "2". [docutils]
+source/index.rst:13: WARNING: Duplicate explicit target name: "label1". [docutils]
+source/index.rst:9: WARNING: Footnote [3] is not referenced. [ref.footnote]
+source/index.rst:10: WARNING: Footnote [*] is not referenced. [ref.footnote]
+source/index.rst:11: WARNING: Footnote [#] is not referenced. [ref.footnote]
+""".strip()