diff --git a/mypy/stubtest.py b/mypy/stubtest.py
index 044412299023..b4447d798cdd 100644
--- a/mypy/stubtest.py
+++ b/mypy/stubtest.py
@@ -344,6 +344,14 @@ class SubClass(runtime):  # type: ignore
         for m in cast(Any, vars)(runtime)
         if not is_probably_private(m) and m not in IGNORABLE_CLASS_DUNDERS
     )
+    # Special-case the __init__ method for Protocols
+    #
+    # TODO: On Python <3.11, __init__ methods on Protocol classes
+    # are silently discarded and replaced.
+    # However, this is not the case on Python 3.11+.
+    # Ideally, we'd figure out a good way of validating Protocol __init__ methods on 3.11+.
+    if stub.is_protocol:
+        to_check.discard("__init__")
 
     for entry in sorted(to_check):
         mangled_entry = entry
@@ -1090,6 +1098,7 @@ def verify_typealias(
     {
         # Special attributes
         "__dict__",
+        "__annotations__",
         "__text_signature__",
         "__weakref__",
         "__del__",  # Only ever called when an object is being deleted, who cares?
diff --git a/mypy/test/teststubtest.py b/mypy/test/teststubtest.py
index 72944f44414c..197669714ad3 100644
--- a/mypy/test/teststubtest.py
+++ b/mypy/test/teststubtest.py
@@ -1033,16 +1033,17 @@ def test_protocol(self) -> Iterator[Case]:
             from typing_extensions import Protocol
 
             class X(Protocol):
+                bar: int
                 def foo(self, x: int, y: bytes = ...) -> str: ...
             """,
             runtime="""
             from typing_extensions import Protocol
 
             class X(Protocol):
+                bar: int
                 def foo(self, x: int, y: bytes = ...) -> str: ...
             """,
-            # TODO: this should not be an error, #12820
-            error="X.__init__"
+            error=None
         )
 
     @collect_cases