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/tiktoken-literal-special-tokens-3a5e7d2b9c4f1a06.yaml b/releasenotes/notes/tiktoken-literal-special-tokens-3a5e7d2b9c4f1a06.yaml
new file mode 100644
index 00000000000..a31ea4de375
--- /dev/null
+++ b/releasenotes/notes/tiktoken-literal-special-tokens-3a5e7d2b9c4f1a06.yaml
@@ -0,0 +1,5 @@
+---
+fixes:
+  - |
+    ``TiktokenCounter`` now counts literal strings such as ``<|endoftext|>`` in messages and tool descriptions
+    as ordinary text instead of raising a ``ValueError``.
diff --git a/test/token_counters/test_tiktoken_counter.py b/test/token_counters/test_tiktoken_counter.py
index bd19f1e5871..e4b279614e1 100644
--- a/test/token_counters/test_tiktoken_counter.py
+++ b/test/token_counters/test_tiktoken_counter.py
@@ -27,7 +27,7 @@ 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]:
         self.encoded.append(text)
         return list(range(len(text.split())))
 
@@ -97,6 +97,14 @@ def test_encodes_the_rendered_conversation(self, fake_encoder):
         assert "<image>" in rendered
         assert "<file: report.pdf>" in rendered
 
+    def test_counts_literal_special_token_in_message(self, fake_encoder):
+        counter = TiktokenCounter()
+
+        count = counter.count([ChatMessage.from_user("Literal <|endoftext|> marker")])
+
+        assert count > 0
+        assert "<|endoftext|>" in fake_encoder.encoded[0]
+
     def test_serde_round_trip(self):
         data = TiktokenCounter(encoding="cl100k_base", tokens_per_image=200, tokens_per_file=3000).to_dict()
 
@@ -131,11 +139,34 @@ def test_nothing_to_measure_is_zero(self):
         assert TiktokenCounter().count([]) == 0
         assert TiktokenCounter().count([], tools=None) == 0
 
+    def test_counts_literal_special_token_in_tool_description(self, fake_encoder):
+        @tool
+        def describe_marker() -> str:
+            """Describe the literal <|endoftext|> marker."""
+            return "marker"
+
+        count = TiktokenCounter().count([], tools=[describe_marker])
+
+        assert count > 0
+        assert "<|endoftext|>" in fake_encoder.encoded[0]
+
 
 @pytest.mark.integration
 class TestTiktokenCounterIntegration:
     """Exercises the real encoder, which downloads its vocabulary on first use."""
 
+    def test_literal_special_token_in_messages_and_tools(self):
+        @tool
+        def describe_marker() -> str:
+            """Explain the literal <|endoftext|> marker."""
+            return "marker"
+
+        counter = TiktokenCounter()
+        messages = [ChatMessage.from_user("Literal <|endoftext|> marker")]
+
+        assert counter.count(messages) > 0
+        assert counter.count(messages, tools=[describe_marker]) > counter.count(messages)
+
     def test_counts_grow_with_content(self):
         counter = TiktokenCounter()