diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index cf4db410925..1c35e0fc2fc 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -10,6 +10,10 @@ Next release
 
 - Improve copyright detection for statements with parens or trailing "authors"
 
+- Fix ``python_version`` environment markers using ``>``, ``!=`` or ``~=`` being
+  silently dropped from the dependency ``extra_data``.
+  https://github.com/aboutcode-org/scancode-toolkit/issues/5309
+
 
 v33.0.0rc1 - 2026-05-14
 ------------------------
diff --git a/src/packagedcode/pypi.py b/src/packagedcode/pypi.py
index dcfd237590e..8eca597382d 100644
--- a/src/packagedcode/pypi.py
+++ b/src/packagedcode/pypi.py
@@ -2278,7 +2278,10 @@ def get_python_version_os(marker):
     requirement Marker or None.
     """
     platform_data = {}
-    python_version_operators = ['<', '>=', '==', '<=', '<']
+    # all comparison operators allowed for a marker in PEP 508
+    python_version_operators = [
+        '<', '<=', '!=', '==', '>=', '>', '~=', '===',
+    ]
 
     if not marker or not isinstance(marker, markers.Marker):
         return platform_data
diff --git a/tests/packagedcode/test_pypi.py b/tests/packagedcode/test_pypi.py
index 20afae813db..297b8771858 100644
--- a/tests/packagedcode/test_pypi.py
+++ b/tests/packagedcode/test_pypi.py
@@ -806,3 +806,21 @@ def test_parse_setup_py(test_loc):
 def test_parse_more_setup_py(test_loc):
     check_setup_py_parsing(test_loc)
 
+
+@pytest.mark.parametrize(
+    ('requirement', 'expected'),
+    [
+        ('requests; python_version < "3.8"', {'python_version': '< 3.8'}),
+        ('requests; python_version <= "3.8"', {'python_version': '<= 3.8'}),
+        ('requests; python_version != "3.8"', {'python_version': '!= 3.8'}),
+        ('requests; python_version == "3.8"', {'python_version': '== 3.8'}),
+        ('requests; python_version >= "3.8"', {'python_version': '>= 3.8'}),
+        ('requests; python_version > "3.8"', {'python_version': '> 3.8'}),
+        ('requests; python_version ~= "3.8"', {'python_version': '~= 3.8'}),
+    ],
+)
+def test_get_python_version_os_handles_all_comparison_operators(requirement, expected):
+    from packvers.requirements import Requirement
+
+    marker = Requirement(requirement).marker
+    assert pypi.get_python_version_os(marker) == expected