diff --git a/haystack/components/builders/chat_prompt_builder.py b/haystack/components/builders/chat_prompt_builder.py
index aba2780fa7..24a5df9efa 100644
--- a/haystack/components/builders/chat_prompt_builder.py
+++ b/haystack/components/builders/chat_prompt_builder.py
@@ -12,7 +12,7 @@
 from haystack import component, default_from_dict, default_to_dict, logging
 from haystack.dataclasses.chat_message import ChatMessage, ChatRole, TextContent
 from haystack.lazy_imports import LazyImport
-from haystack.utils import Jinja2TimeExtension
+from haystack.utils import Jinja2TemplateVariableExtractor, Jinja2TimeExtension
 from haystack.utils.jinja2_chat_extension import ChatMessageExtension, templatize_part
 
 logger = logging.getLogger(__name__)
@@ -171,21 +171,31 @@ def __init__(
 
         extracted_variables = []
         if template and not variables:
+
+            def _extract_from_text(
+                text: Optional[str], role: Optional[str] = None, is_filter_allowed: bool = False
+            ) -> list:
+                if text is None:
+                    raise ValueError(NO_TEXT_ERROR_MESSAGE.format(role=role or "unknown", message=text))
+                if is_filter_allowed and "templatize_part" in text:
+                    raise ValueError(FILTER_NOT_ALLOWED_ERROR_MESSAGE)
+
+                ast = self._env.parse(text)
+                template_variables = meta.find_undeclared_variables(ast)
+                jinja_var_extractor = Jinja2TemplateVariableExtractor(env=self._env)
+                assigned_variables = jinja_var_extractor._extract_from_text(template_str=text)
+                return list(template_variables - assigned_variables)
+
             if isinstance(template, list):
                 for message in template:
                     if message.is_from(ChatRole.USER) or message.is_from(ChatRole.SYSTEM):
-                        # infer variables from template
-                        if message.text is None:
-                            raise ValueError(NO_TEXT_ERROR_MESSAGE.format(role=message.role.value, message=message))
-                        if message.text and "templatize_part" in message.text:
-                            raise ValueError(FILTER_NOT_ALLOWED_ERROR_MESSAGE)
-                        ast = self._env.parse(message.text)
-                        template_variables = meta.find_undeclared_variables(ast)
-                        extracted_variables += list(template_variables)
+                        extracted_variables += _extract_from_text(
+                            message.text, role=message.role.value, is_filter_allowed=True
+                        )
             elif isinstance(template, str):
-                ast = self._env.parse(template)
-                extracted_variables = list(meta.find_undeclared_variables(ast))
+                extracted_variables = _extract_from_text(template, is_filter_allowed=False)
 
+        extracted_variables = extracted_variables or []
         self.variables = variables or extracted_variables
         self.required_variables = required_variables or []
 
diff --git a/haystack/components/builders/prompt_builder.py b/haystack/components/builders/prompt_builder.py
index 3e1d3603ca..ab2caea1f3 100644
--- a/haystack/components/builders/prompt_builder.py
+++ b/haystack/components/builders/prompt_builder.py
@@ -8,7 +8,7 @@
 from jinja2.sandbox import SandboxedEnvironment
 
 from haystack import component, default_to_dict, logging
-from haystack.utils import Jinja2TimeExtension
+from haystack.utils import Jinja2TemplateVariableExtractor, Jinja2TimeExtension
 
 logger = logging.getLogger(__name__)
 
@@ -174,11 +174,15 @@ def __init__(
             self._env = SandboxedEnvironment()
 
         self.template = self._env.from_string(template)
+
         if not variables:
-            # infer variables from template
             ast = self._env.parse(template)
             template_variables = meta.find_undeclared_variables(ast)
-            variables = list(template_variables)
+            jinja_var_extractor = Jinja2TemplateVariableExtractor(env=self._env)
+            assigned_variables = jinja_var_extractor._extract_from_text(template_str=template)
+
+            variables = list(template_variables - assigned_variables)
+
         variables = variables or []
         self.variables = variables
 
diff --git a/haystack/utils/__init__.py b/haystack/utils/__init__.py
index 7439e97658..3b8edaa6bc 100644
--- a/haystack/utils/__init__.py
+++ b/haystack/utils/__init__.py
@@ -15,6 +15,7 @@
     "device": ["ComponentDevice", "Device", "DeviceMap", "DeviceType"],
     "deserialization": ["deserialize_document_store_in_init_params_inplace", "deserialize_chatgenerator_inplace"],
     "filters": ["document_matches_filter", "raise_on_invalid_filter_syntax"],
+    "jinja2": ["Jinja2TemplateVariableExtractor"],
     "jinja2_extensions": ["Jinja2TimeExtension"],
     "jupyter": ["is_in_jupyter"],
     "misc": ["expit", "expand_page_range"],
@@ -40,6 +41,7 @@
     from .device import DeviceType as DeviceType
     from .filters import document_matches_filter as document_matches_filter
     from .filters import raise_on_invalid_filter_syntax as raise_on_invalid_filter_syntax
+    from .jinja2 import Jinja2TemplateVariableExtractor as Jinja2TemplateVariableExtractor
     from .jinja2_extensions import Jinja2TimeExtension as Jinja2TimeExtension
     from .jupyter import is_in_jupyter as is_in_jupyter
     from .misc import expand_page_range as expand_page_range
diff --git a/haystack/utils/jinja2.py b/haystack/utils/jinja2.py
new file mode 100644
index 0000000000..60d9838896
--- /dev/null
+++ b/haystack/utils/jinja2.py
@@ -0,0 +1,44 @@
+# SPDX-FileCopyrightText: 2022-present deepset GmbH <info@deepset.ai>
+#
+# SPDX-License-Identifier: Apache-2.0
+
+from typing import Optional
+
+from jinja2 import Environment, nodes
+
+
+class Jinja2TemplateVariableExtractor:
+    """
+    A utility class for extracting declared variables from Jinja2 templates.
+    """
+
+    def __init__(self, env: Optional[Environment] = None):
+        self.env = env or Environment()
+
+    def _extract_from_text(self, template_str: str, role: Optional[str] = None) -> set[str]:
+        """
+        Extract declared variables from a Jinja2 template string.
+
+        :param template_str: The Jinja2 template string to analyze.
+        :param env: The Jinja2 Environment. Defaults to None.
+
+        :returns:
+        A set of variable names used in the template.
+        """
+        try:
+            ast = self.env.parse(template_str)
+        except Exception as e:
+            raise RuntimeError(f"Failed to parse Jinja2 template: {e}")
+
+        # Collect all variables assigned inside the template via {% set %}
+        assigned_variables = set()
+
+        for node in ast.find_all(nodes.Assign):
+            if isinstance(node.target, nodes.Name):
+                assigned_variables.add(node.target.name)
+            elif isinstance(node.target, (nodes.List, nodes.Tuple)):
+                for name_node in node.target.items:
+                    if isinstance(name_node, nodes.Name):
+                        assigned_variables.add(name_node.name)
+
+        return assigned_variables
diff --git a/releasenotes/notes/jinja2-set-vars-parsing-919ae03d3c8a1465.yaml b/releasenotes/notes/jinja2-set-vars-parsing-919ae03d3c8a1465.yaml
new file mode 100644
index 0000000000..a617094f1f
--- /dev/null
+++ b/releasenotes/notes/jinja2-set-vars-parsing-919ae03d3c8a1465.yaml
@@ -0,0 +1,7 @@
+fixes:
+  - |
+    Fixed an issue where Jinja2 variable assignments using the `set` directive
+    were not being parsed correctly in certain contexts. This fix ensures that
+    variables assigned with `{% set var = value %}` are now properly recognized
+    and can be used as expected within templates inside `PromptBuilder` and
+    `ChatPromptBuilder`.
diff --git a/test/components/builders/test_chat_prompt_builder.py b/test/components/builders/test_chat_prompt_builder.py
index fa15dcbc56..99efedff92 100644
--- a/test/components/builders/test_chat_prompt_builder.py
+++ b/test/components/builders/test_chat_prompt_builder.py
@@ -957,3 +957,31 @@ def test_from_dict(self):
         assert builder.template == template
         assert builder.variables == ["name", "assistant_name"]
         assert builder.required_variables == ["name"]
+
+    def test_variables_correct_with_tuple_assignment(self):
+        template = """{% if existing_documents is not none %}
+    {% set x, y = (existing_documents|length, 1) %}
+    {% else %}
+    {% set x, y = (0, 1) %}
+    {% endif %}
+    {% message role="user" %}x={{ x }}, y={{ y }}{% endmessage %}
+    """
+        builder = ChatPromptBuilder(template=template, required_variables="*")
+        assert set(builder.variables) == {"existing_documents"}
+        res = builder.run(existing_documents=None)
+        prompt = res["prompt"]
+        assert any("x=0, y=1" in msg.text for msg in prompt)
+
+    def test_variables_correct_with_list_assignment(self):
+        template = """{% if existing_documents is not none %}
+    {% set x, y = [existing_documents|length, 1] %}
+    {% else %}
+    {% set x, y = [0, 1] %}
+    {% endif %}
+    {% message role="user" %}x={{ x }}, y={{ y }}{% endmessage %}
+    """
+        builder = ChatPromptBuilder(template=template, required_variables="*")
+        assert set(builder.variables) == {"existing_documents"}
+        res = builder.run(existing_documents=None)
+        prompt = res["prompt"]
+        assert any("x=0, y=1" in msg.text for msg in prompt)
diff --git a/test/components/builders/test_prompt_builder.py b/test/components/builders/test_prompt_builder.py
index 8a5504c5fc..288d0f2554 100644
--- a/test/components/builders/test_prompt_builder.py
+++ b/test/components/builders/test_prompt_builder.py
@@ -337,3 +337,47 @@ def test_warning_no_required_variables(self, caplog):
         with caplog.at_level(logging.WARNING):
             _ = PromptBuilder(template="This is a {{ variable }}")
             assert "but `required_variables` is not set." in caplog.text
+
+    def test_template_assigned_variables_from_required_inputs(self) -> None:
+        template = """{% if existing_documents is not none %}
+                   {% set existing_doc_len = existing_documents|length %}
+                   {% else %}
+                   {% set existing_doc_len = 0 %}
+                   {% endif %}
+                   {% for doc in docs %}
+                   <document reference="{{loop.index + existing_doc_len}}">
+                    {{ doc.content }}
+                    </document>
+                   {% endfor %}
+                   """
+
+        builder = PromptBuilder(template=template, required_variables="*")
+
+        builder = PromptBuilder(template=template, required_variables="*")
+        assert set(builder.variables) == {"docs", "existing_documents"}
+
+    def test_variables_correct_with_tuple_assignment(self):
+        template = """{% if existing_documents is not none %}
+{% set x, y = (existing_documents|length, 1) %}
+{% else %}
+{% set x, y = (0, 1) %}
+{% endif %}
+x={{ x }}, y={{ y }}
+"""
+        builder = PromptBuilder(template=template, required_variables="*")
+        assert set(builder.variables) == {"existing_documents"}
+        res = builder.run(existing_documents=None)
+        assert "x=0, y=1" in res["prompt"]
+
+    def test_variables_correct_with_list_assignment(self):
+        template = """{% if existing_documents is not none %}
+{% set x, y = [existing_documents|length, 1] %}
+{% else %}
+{% set x, y = [0, 1] %}
+{% endif %}
+x={{ x }}, y={{ y }}
+"""
+        builder = PromptBuilder(template=template, required_variables="*")
+        assert set(builder.variables) == {"existing_documents"}
+        res = builder.run(existing_documents=None)
+        assert "x=0, y=1" in res["prompt"]