diff --git a/haystack/token_counters/tiktoken_counter.py b/haystack/token_counters/tiktoken_counter.py
index 57298234074..f505b89bf99 100644
--- a/haystack/token_counters/tiktoken_counter.py
+++ b/haystack/token_counters/tiktoken_counter.py
@@ -74,7 +74,7 @@ def count(self, messages: list[ChatMessage], tools: ToolsType | None = None) ->
         if not messages and not tools:
             return 0
         self.warm_up()
-        text_tokens = len(self._encoder.encode(_rendered_conversation(messages) + _rendered_tools(tools)))
+        text_tokens = len(self._encoder.encode_ordinary(_rendered_conversation(messages) + _rendered_tools(tools)))
         return text_tokens + _non_text_tokens(
             messages, tokens_per_image=self.tokens_per_image, tokens_per_file=self.tokens_per_file
         )
diff --git a/releasenotes/notes/Fix-TiktokenCounter-crash-on-literal-special-token-strings-9c0c75f8a3e03c50.yaml b/releasenotes/notes/Fix-TiktokenCounter-crash-on-literal-special-token-strings-9c0c75f8a3e03c50.yaml
new file mode 100644
index 00000000000..b7aa0412f49
--- /dev/null
+++ b/releasenotes/notes/Fix-TiktokenCounter-crash-on-literal-special-token-strings-9c0c75f8a3e03c50.yaml
@@ -0,0 +1,8 @@
+---
+fixes:
+  - |
+    Fix ``TiktokenCounter`` crashing with ``ValueError`` when messages or
+    tool schemas contain literal special-token strings such as
+    ``<|endoftext|>``. Counting now uses ``encode_ordinary``, matching the
+    earlier fix for the document splitters in `#12853
+    <https://github.com/deepset-ai/haystack/issues/12853>`_.
diff --git a/test/token_counters/test_tiktoken_counter.py b/test/token_counters/test_tiktoken_counter.py
index bd19f1e5871..bc78f6d8083 100644
--- a/test/token_counters/test_tiktoken_counter.py
+++ b/test/token_counters/test_tiktoken_counter.py
@@ -27,7 +27,10 @@ class _FakeEncoder:
     def __init__(self) -> None:
         self.encoded: list[str] = []
 
-    def encode(self, text: str) -> list[int]:
+    def encode_ordinary(self, text: str) -> list[int]:
+        # Mirrors `tiktoken.Encoding.encode_ordinary`: literal special-token
+        # markers (e.g. `<|endoftext|>`) are counted as ordinary text and
+        # must never raise. See https://github.com/deepset-ai/haystack/issues/12869
         self.encoded.append(text)
         return list(range(len(text.split())))
 
@@ -131,6 +134,13 @@ def test_nothing_to_measure_is_zero(self):
         assert TiktokenCounter().count([]) == 0
         assert TiktokenCounter().count([], tools=None) == 0
 
+    def test_special_token_markers_are_counted_as_ordinary_text(self, fake_encoder):
+        # https://github.com/deepset-ai/haystack/issues/12869 — `encode()`
+        # raises on literal `<|endoftext|>`; `encode_ordinary()` must not.
+        messages = [ChatMessage.from_user("score <|endoftext|> now")]
+        assert TiktokenCounter().count(messages) > 0
+        assert "<|endoftext|>" in fake_encoder.encoded[0]
+
 
 @pytest.mark.integration
 class TestTiktokenCounterIntegration: