diff --git a/api/core/app/apps/base_app_generator.py b/api/core/app/apps/base_app_generator.py
index 1c6ca87925..1b0474142e 100644
--- a/api/core/app/apps/base_app_generator.py
+++ b/api/core/app/apps/base_app_generator.py
@@ -99,6 +99,15 @@ class BaseAppGenerator:
             if value is None:
                 return None
 
+        # Treat empty placeholders for optional file inputs as unset
+        if (
+            variable_entity.type in {VariableEntityType.FILE, VariableEntityType.FILE_LIST}
+            and not variable_entity.required
+        ):
+            # Treat empty string (frontend default) or empty list as unset
+            if not value and isinstance(value, (str, list)):
+                return None
+
         if variable_entity.type in {
             VariableEntityType.TEXT_INPUT,
             VariableEntityType.SELECT,
diff --git a/api/tests/unit_tests/core/app/apps/test_base_app_generator.py b/api/tests/unit_tests/core/app/apps/test_base_app_generator.py
index fdab39f133..d622c3a555 100644
--- a/api/tests/unit_tests/core/app/apps/test_base_app_generator.py
+++ b/api/tests/unit_tests/core/app/apps/test_base_app_generator.py
@@ -265,3 +265,82 @@ def test_validate_inputs_with_default_value():
     )
 
     assert result == [{"id": "file1", "name": "doc1.pdf"}, {"id": "file2", "name": "doc2.pdf"}]
+
+
+def test_validate_inputs_optional_file_with_empty_string():
+    """Test that optional FILE variable with empty string returns None"""
+    base_app_generator = BaseAppGenerator()
+
+    var_file = VariableEntity(
+        variable="test_file",
+        label="test_file",
+        type=VariableEntityType.FILE,
+        required=False,
+    )
+
+    result = base_app_generator._validate_inputs(
+        variable_entity=var_file,
+        value="",
+    )
+
+    assert result is None
+
+
+def test_validate_inputs_optional_file_list_with_empty_list():
+    """Test that optional FILE_LIST variable with empty list returns None"""
+    base_app_generator = BaseAppGenerator()
+
+    var_file_list = VariableEntity(
+        variable="test_file_list",
+        label="test_file_list",
+        type=VariableEntityType.FILE_LIST,
+        required=False,
+    )
+
+    result = base_app_generator._validate_inputs(
+        variable_entity=var_file_list,
+        value=[],
+    )
+
+    assert result is None
+
+
+def test_validate_inputs_required_file_with_empty_string_fails():
+    """Test that required FILE variable with empty string still fails validation"""
+    base_app_generator = BaseAppGenerator()
+
+    var_file = VariableEntity(
+        variable="test_file",
+        label="test_file",
+        type=VariableEntityType.FILE,
+        required=True,
+    )
+
+    with pytest.raises(ValueError) as exc_info:
+        base_app_generator._validate_inputs(
+            variable_entity=var_file,
+            value="",
+        )
+
+    assert "must be a file" in str(exc_info.value)
+
+
+def test_validate_inputs_optional_file_with_empty_string_ignores_default():
+    """Test that optional FILE variable with empty string returns None, not the default"""
+    base_app_generator = BaseAppGenerator()
+
+    var_file = VariableEntity(
+        variable="test_file",
+        label="test_file",
+        type=VariableEntityType.FILE,
+        required=False,
+        default={"id": "file123", "name": "default.pdf"},
+    )
+
+    # When value is empty string (from frontend), should return None, not default
+    result = base_app_generator._validate_inputs(
+        variable_entity=var_file,
+        value="",
+    )
+
+    assert result is None