diff --git a/api/python/quilt3/data_transfer.py b/api/python/quilt3/data_transfer.py
index 219c584de57..447d8ca46a0 100644
--- a/api/python/quilt3/data_transfer.py
+++ b/api/python/quilt3/data_transfer.py
@@ -876,7 +876,7 @@ def copy_file(src: PhysicalKey, dest: PhysicalKey, size=None, message=None, call
     """
     def sanity_check(rel_path):
         for part in rel_path.split('/'):
-            if part in ('', '.', '..'):
+            if part in ('.', '..'):
                 raise ValueError("Invalid relative path: %r" % rel_path)
 
     url_list = []
diff --git a/api/python/quilt3/util.py b/api/python/quilt3/util.py
index 2124d300692..b52ecf52356 100644
--- a/api/python/quilt3/util.py
+++ b/api/python/quilt3/util.py
@@ -139,8 +139,6 @@ def __init__(self, bucket, path, version_id):
             assert version_id is None, "Local keys cannot have a version ID"
             if os.name == 'nt':
                 assert '\\' not in path, "Paths must use / as a separator"
-        else:
-            assert not path.startswith('/'), "S3 paths must not start with '/'"
 
         self.bucket = bucket
         self.path = path
diff --git a/api/python/tests/integration/test_packages.py b/api/python/tests/integration/test_packages.py
index b9e92c1e5f7..3766ab97c56 100644
--- a/api/python/tests/integration/test_packages.py
+++ b/api/python/tests/integration/test_packages.py
@@ -623,6 +623,15 @@ def test_s3_set_dir(self):
 
             list_object_versions_mock.assert_called_with('bucket', 'foo/')
 
+    def test_set_dir_root_folder_named_slash(self):
+        with patch('quilt3.packages.list_object_versions') as list_object_versions_mock:
+            list_object_versions_mock.return_value = ([
+                dict(Key='/foo/a.txt', VersionId='xyz', IsLatest=True, Size=10),
+            ], [])
+            pkg = Package()
+            pkg.set_dir('bar', 's3://bucket//foo')  # top-level '/' folder
+            assert True, "No exception raised for top-level folder named '/'"
+
     def test_set_dir_wrong_update_policy(self):
         """Verify non existing update policy raises value error."""
         pkg = Package()
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index c4eed9428d6..4eae09aa162 100644
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -13,6 +13,12 @@ Entries inside each section should be ordered by type:
 ## CLI
 !-->
 
+# unreleased - YYYY-MM-DD
+
+## Python API
+
+* [Fixed] Allow S3 paths starting with `/` in `Package().set_dir()` ([#4207](https://github.com/quiltdata/quilt/pull/4207))
+
 # 6.1.0 - 2024-10-14
 
 ## Python API