diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
index 341349836..92ee9d4db 100644
--- a/docs/CHANGELOG.rst
+++ b/docs/CHANGELOG.rst
@@ -6,6 +6,15 @@ All notable changes to this project are documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
 
+==========
+Unreleased
+==========
+
+Fixed
+-----
+- Fix crash in ``get_annotation`` when delete marker is set
+
+
 ===================
 42.0.0 - 2024-11-21
 ===================
diff --git a/resolwe/flow/models/entity.py b/resolwe/flow/models/entity.py
index febcef652..7b9bedf12 100644
--- a/resolwe/flow/models/entity.py
+++ b/resolwe/flow/models/entity.py
@@ -210,9 +210,13 @@ def get_annotation(self, path: str, default: Any = None) -> Any:
         :return: value of the annotation or default if not found.
         """
         group_name, field_name = path.split(".", maxsplit=1)
-        annotation: AnnotationValue = self.annotations.filter(
-            field__group__name=group_name, field__name=field_name
-        ).first()
+        annotation: AnnotationValue = (
+            self.annotations.filter(
+                field__group__name=group_name, field__name=field_name
+            )
+            .remove_delete_markers()
+            .first()
+        )
         return annotation.value if annotation else default
 
     def set_annotation(self, path: str, value: Any, contributor=None):
diff --git a/resolwe/flow/tests/test_annotations.py b/resolwe/flow/tests/test_annotations.py
index 9a3aaf9ee..4c6bc7147 100644
--- a/resolwe/flow/tests/test_annotations.py
+++ b/resolwe/flow/tests/test_annotations.py
@@ -40,21 +40,38 @@ class AnnotationValueTest(TestCase):
     def setUp(self):
         """Prepare the test entity and annotation values."""
         super().setUp()
-        entity: Entity = Entity.objects.create(
+        self.entity: Entity = Entity.objects.create(
             name="Entity", contributor=self.contributor
         )
         annotation_group: AnnotationGroup = AnnotationGroup.objects.create(
             name="group", label="Annotation group", sort_order=1
         )
         self.field = AnnotationField.objects.create(
-            name="Field 1",
+            name="field_1",
             label="Field 1 label",
             type=AnnotationType.STRING.value,
             sort_order=1,
             group=annotation_group,
         )
         self.value = AnnotationValue.objects.create(
-            entity=entity, field=self.field, value="Test", contributor=self.contributor
+            entity=self.entity,
+            field=self.field,
+            value="Test",
+            contributor=self.contributor,
+        )
+
+    def test_get_annotation(self):
+        self.assertEqual(self.entity.get_annotation("group.field_1"), "Test")
+        # Create delete marker and test again.
+        AnnotationValue.objects.create(
+            entity=self.entity,
+            field=self.field,
+            _value=None,
+            contributor=self.contributor,
+        )
+        self.assertIsNone(self.entity.get_annotation("group.field_1"))
+        self.assertEqual(
+            self.entity.get_annotation("group.field_1", "default"), "default"
         )
 
     def test_protected(self):