diff --git a/jupyter_server/base/call_context.py b/jupyter_server/base/call_context.py
index 4e80be8a7d..13f6a762ed 100644
--- a/jupyter_server/base/call_context.py
+++ b/jupyter_server/base/call_context.py
@@ -41,7 +41,6 @@ def get(cls, name: str) -> Any:
             The value associated with the named variable for this call context
         """
         name_value_map = CallContext._get_map()
-
         if name in name_value_map:
             return name_value_map[name]
         return None  # TODO: should this raise `LookupError` (or a custom error derived from said)
@@ -61,8 +60,9 @@ def set(cls, name: str, value: Any) -> None:
         -------
         None
         """
-        name_value_map = CallContext._get_map()
+        name_value_map = CallContext._get_map().copy()
         name_value_map[name] = value
+        CallContext._name_value_map.set(name_value_map)
 
     @classmethod
     def context_variable_names(cls) -> list[str]:
diff --git a/tests/base/test_call_context.py b/tests/base/test_call_context.py
index 1c12338d61..f3e48522f5 100644
--- a/tests/base/test_call_context.py
+++ b/tests/base/test_call_context.py
@@ -1,4 +1,5 @@
 import asyncio
+from contextvars import copy_context
 
 from jupyter_server import CallContext
 from jupyter_server.auth.utils import get_anonymous_username
@@ -107,3 +108,39 @@ async def context2():
     # Assert that THIS context doesn't have any variables defined.
     names = CallContext.context_variable_names()
     assert len(names) == 0
+
+
+async def test_callcontext_with_copy_context_run():
+    """
+    Test scenario:
+    - The upper layer uses copy_context().run()
+    - Multiple contexts concurrently modify CallContext
+    - Verify that no context pollution occurs
+    """
+
+    async def context_task(name, value, delay):
+        """Coroutine task that modifies CallContext and validates its own values"""
+        await asyncio.sleep(delay)
+        CallContext.set(name, value)
+        # Sleep again to simulate interleaving execution
+        await asyncio.sleep(0.1)
+        assert CallContext.get(name) == value, f"{name} was polluted"
+        # Ensure only the variable written by this context exists
+        keys = CallContext.context_variable_names()
+        assert name in keys
+        assert len(keys) == 1
+
+    # Initialize a variable in the main context
+    CallContext.set("foo", "bar3")
+
+    # Create two independent copy_context instances
+    ctx1 = copy_context()
+    ctx2 = copy_context()
+
+    # Run coroutines in their respective contexts
+    fut1 = asyncio.create_task(ctx1.run(lambda: context_task("foo", "bar1", 0.0)))
+    fut2 = asyncio.create_task(ctx2.run(lambda: context_task("foo", "bar2", 0.05)))
+    await asyncio.gather(fut1, fut2)
+
+    # The main context should remain unaffected (still is empty)
+    assert CallContext.get("foo") == "bar3"