diff --git a/buildscripts/idl/idl/parser.py b/buildscripts/idl/idl/parser.py
index 41b73966d26..2838b6baaba 100644
--- a/buildscripts/idl/idl/parser.py
+++ b/buildscripts/idl/idl/parser.py
@@ -1059,11 +1059,13 @@ def _propagate_globals(spec):
         idltype.cpp_type = _prefix_with_namespace(cpp_namespace, idltype.cpp_type)
 
 
-def parse_file(stream, error_file_name):
-    # type: (Any, str) -> syntax.IDLParsedSpec
+def parse_file(stream, error_file_name, parse_feature_flags=True):
+    # type: (Any, str, bool) -> syntax.IDLParsedSpec
     """
     Parse a YAML document into an idl.syntax tree.
 
+    If parse_feature_flags is False, don't attempt to parse the feature flag type.
+
     stream: is a io.Stream.
     error_file_name: just a file name for error messages to use.
     """
@@ -1116,8 +1118,10 @@ def parse_file(stream, error_file_name):
             _parse_mapping(ctxt, spec, second_node, "server_parameters", _parse_server_parameter)
         elif first_name == "configs":
             _parse_mapping(ctxt, spec, second_node, "configs", _parse_config_option)
-        elif first_name == "feature_flags":
+        elif parse_feature_flags and first_name == "feature_flags":
             _parse_mapping(ctxt, spec, second_node, "feature_flags", _parse_feature_flag)
+        elif not parse_feature_flags and first_name == "feature_flags":
+            continue
         else:
             ctxt.add_unknown_root_node_error(first_node)
 
@@ -1152,16 +1156,18 @@ class ImportResolverBase(object, metaclass=ABCMeta):
         pass
 
 
-def parse(stream, input_file_name, resolver):
-    # type: (Any, str, ImportResolverBase) -> syntax.IDLParsedSpec
+def parse(stream, input_file_name, resolver, parse_feature_flags=True):
+    # type: (Any, str, ImportResolverBase, bool) -> syntax.IDLParsedSpec
     """
     Parse a YAML document into an idl.syntax tree.
 
+    If parse_feature_flags is False, don't attempt to parse the feature flag type.
+
     stream: is a io.Stream.
     input_file_name: a file name for error messages to use, and to help resolve imported files.
     """
 
-    root_doc = parse_file(stream, input_file_name)
+    root_doc = parse_file(stream, input_file_name, parse_feature_flags)
 
     if root_doc.errors:
         return root_doc
@@ -1198,7 +1204,7 @@ def parse(stream, input_file_name, resolver):
 
         # Parse imported file
         with resolver.open(resolved_file_name) as file_stream:
-            parsed_doc = parse_file(file_stream, resolved_file_name)
+            parsed_doc = parse_file(file_stream, resolved_file_name, parse_feature_flags)
 
         # Check for errors
         if parsed_doc.errors:
diff --git a/buildscripts/idl/idl_check_compatibility.py b/buildscripts/idl/idl_check_compatibility.py
index 76ce7de7475..0a1d8fe01a5 100644
--- a/buildscripts/idl/idl_check_compatibility.py
+++ b/buildscripts/idl/idl_check_compatibility.py
@@ -422,7 +422,7 @@ def get_new_commands(
             with open(new_idl_file_path) as new_file:
                 new_idl_file = parser.parse(
                     new_file, new_idl_file_path,
-                    CompilerImportResolver(import_directories + [new_idl_dir]))
+                    CompilerImportResolver(import_directories + [new_idl_dir]), False)
                 if new_idl_file.errors:
                     new_idl_file.errors.dump_errors()
                     raise ValueError(f"Cannot parse {new_idl_file_path}")
@@ -1310,9 +1310,11 @@ def check_error_reply(old_basic_types_path: str, new_basic_types_path: str,
     ctxt = IDLCompatibilityContext(old_idl_dir, new_idl_dir, IDLCompatibilityErrorCollection())
     with open(old_basic_types_path) as old_file:
         old_idl_file = parser.parse(old_file, old_basic_types_path,
-                                    CompilerImportResolver(old_import_directories))
+                                    CompilerImportResolver(old_import_directories), False)
         if old_idl_file.errors:
             old_idl_file.errors.dump_errors()
+            # If parsing old IDL files fails, it might be because the parser has been recently
+            # updated to require something that isn't present in older IDL files.
             raise ValueError(f"Cannot parse {old_basic_types_path}")
 
         old_error_reply_struct = old_idl_file.spec.symbols.get_struct("ErrorReply")
@@ -1322,7 +1324,7 @@ def check_error_reply(old_basic_types_path: str, new_basic_types_path: str,
         else:
             with open(new_basic_types_path) as new_file:
                 new_idl_file = parser.parse(new_file, new_basic_types_path,
-                                            CompilerImportResolver(new_import_directories))
+                                            CompilerImportResolver(new_import_directories), False)
                 if new_idl_file.errors:
                     new_idl_file.errors.dump_errors()
                     raise ValueError(f"Cannot parse {new_basic_types_path}")
@@ -1490,9 +1492,11 @@ def check_compatibility(old_idl_dir: str, new_idl_dir: str, old_import_directori
             with open(old_idl_file_path) as old_file:
                 old_idl_file = parser.parse(
                     old_file, old_idl_file_path,
-                    CompilerImportResolver(old_import_directories + [old_idl_dir]))
+                    CompilerImportResolver(old_import_directories + [old_idl_dir]), False)
                 if old_idl_file.errors:
                     old_idl_file.errors.dump_errors()
+                    # If parsing old IDL files fails, it might be because the parser has been
+                    # recently updated to require something that isn't present in older IDL files.
                     raise ValueError(f"Cannot parse {old_idl_file_path}")
 
                 for old_cmd in old_idl_file.spec.symbols.commands:
@@ -1559,7 +1563,7 @@ def get_generic_arguments(gen_args_file_path: str, includes: str) -> Tuple[Set[s
 
     with open(gen_args_file_path) as gen_args_file:
         parsed_idl_file = parser.parse(gen_args_file, gen_args_file_path,
-                                       CompilerImportResolver(includes))
+                                       CompilerImportResolver(includes), False)
         if parsed_idl_file.errors:
             parsed_idl_file.errors.dump_errors()
             raise ValueError(f"Cannot parse {gen_args_file_path}")
diff --git a/etc/evergreen.yml b/etc/evergreen.yml
index 76f3acb8451..2cd1f30c336 100644
--- a/etc/evergreen.yml
+++ b/etc/evergreen.yml
@@ -1065,9 +1065,7 @@ buildvariants:
   - name: compile_integration_and_test_parallel_stream_TG
     distros:
     - rhel80-large
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   - name: .aggfuzzer !.feature_flag_guarded !.no_debug_mode
   - name: .aggregation !.feature_flag_guarded !.no_debug_mode
   - name: audit
@@ -1197,9 +1195,7 @@ buildvariants:
   - name: analyze_shard_key_jscore_passthrough_gen
   - name: query_golden_classic
   - name: lint_fuzzer_sanity_patch
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   # - name: burn_in_tasks_gen
   #   depends_on:
   #   - name: version_burn_in_gen
@@ -1427,9 +1423,7 @@ buildvariants:
   - name: secondary_reads_passthrough_gen
   - name: session_jscore_passthrough
   - name: sharding_api_version_jscore_passthrough_gen
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   - name: unittest_shell_hang_analyzer_gen
   - name: vector_search
   - name: vector_search_auth
@@ -1460,9 +1454,7 @@ buildvariants:
   - name: analyze_shard_key_jscore_passthrough_gen
   - name: .cqf
   - name: lint_fuzzer_sanity_patch
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   # - name: burn_in_tasks_gen
   #   depends_on:
   #   - name: version_burn_in_gen
@@ -1962,9 +1954,7 @@ buildvariants:
   - name: analyze_shard_key_jscore_passthrough_gen
   - name: query_golden_classic
   - name: lint_fuzzer_sanity_patch
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   - name: check_feature_flag_tags
   - name: check_for_todos
   - name: .aggfuzzer !.cqf_only
@@ -2871,9 +2861,7 @@ buildvariants:
     distros:
     - amazon2-arm64-large
   - name: .lint
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   - name: validate_commit_message
   - name: lint_large_files_check
   - name: check_feature_flag_tags
@@ -2927,9 +2915,7 @@ buildvariants:
   - name: analyze_shard_key_jscore_passthrough_gen
   - name: query_golden_classic
   - name: lint_fuzzer_sanity_patch
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   - name: check_feature_flag_tags
   - name: check_for_todos
   - name: .aggfuzzer !.cqf_only !.feature_flag_guarded
diff --git a/etc/evergreen_yml_components/variants/classic_engine.yml b/etc/evergreen_yml_components/variants/classic_engine.yml
index a9a43c5b96f..d0d39b61c07 100644
--- a/etc/evergreen_yml_components/variants/classic_engine.yml
+++ b/etc/evergreen_yml_components/variants/classic_engine.yml
@@ -166,9 +166,7 @@ buildvariants:
   - name: secondary_reads_passthrough_gen
   - name: session_jscore_passthrough
   - name: sharding_api_version_jscore_passthrough_gen
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   - name: unittest_shell_hang_analyzer_gen
   - name: vector_search
   - name: vector_search_auth
diff --git a/etc/evergreen_yml_components/variants/misc_release.yml b/etc/evergreen_yml_components/variants/misc_release.yml
index ca4cd1212f7..be4efb1dd12 100644
--- a/etc/evergreen_yml_components/variants/misc_release.yml
+++ b/etc/evergreen_yml_components/variants/misc_release.yml
@@ -225,9 +225,7 @@ buildvariants:
   - name: compile_integration_and_test_parallel_stream_TG
     distros:
     - amazon2-arm64-large
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   - name: .aggfuzzer !.feature_flag_guarded
   - name: .aggregation !.feature_flag_guarded
   - name: audit
@@ -387,9 +385,7 @@ buildvariants:
   - name: compile_test_and_package_serial_no_unittests_TG
     distros:
     - amazon2023.0-large
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   - name: .aggfuzzer !.feature_flag_guarded !.multiversion
   - name: .aggregation !.feature_flag_guarded
   - name: audit
@@ -547,9 +543,7 @@ buildvariants:
   - name: compile_test_and_package_serial_no_unittests_TG
     distros:
     - amazon2023.0-arm64-large
-  # TODO (SERVER-79361): Re-enable the IDL compatibility checker once the
-  # IDL compiler issue has been resolved.
-  # - name: test_api_version_compatibility
+  - name: test_api_version_compatibility
   - name: .aggfuzzer !.feature_flag_guarded !.multiversion
   - name: .aggregation !.feature_flag_guarded
   - name: audit
diff --git a/evergreen/check_idl_compat.sh b/evergreen/check_idl_compat.sh
index cfb83ccd6b1..5566cf23dbd 100755
--- a/evergreen/check_idl_compat.sh
+++ b/evergreen/check_idl_compat.sh
@@ -7,34 +7,31 @@ set -o errexit
 set -o verbose
 activate_venv
 
-# TODO (SERVER-79361): Re-enable this code once the IDL compiler issue has been resolved
-# for the IDL compatibility script.
+$python buildscripts/idl/check_stable_api_commands_have_idl_definitions.py -v --install-dir dist-test/bin --include src --include src/mongo/db/modules/enterprise/src 1
+$python buildscripts/idl/checkout_idl_files_from_past_releases.py -v idls
 
-# $python buildscripts/idl/check_stable_api_commands_have_idl_definitions.py -v --install-dir dist-test/bin --include src --include src/mongo/db/modules/enterprise/src 1
-# $python buildscripts/idl/checkout_idl_files_from_past_releases.py -v idls
+function run_idl_check_compatibility {
+  dir=$1
+  output=$(
+    python buildscripts/idl/idl_check_compatibility.py -v \
+      --old-include "$dir/src" \
+      --old-include "$dir/src/mongo/db/modules/enterprise/src" \
+      --new-include src \
+      --new-include src/mongo/db/modules/enterprise/src \
+      "$dir/src" src
+  )
+  exit_code=$?
+  echo "Performing idl check compatibility with release: $dir:"
+  echo "$output"
+  if [ $exit_code -ne 0 ]; then
+    exit 255
+  fi
+}
+export -f run_idl_check_compatibility
+find idls -maxdepth 1 -mindepth 1 -type d | xargs -n 1 -P 0 -I % bash -c 'run_idl_check_compatibility "$@"' _ %
 
-# function run_idl_check_compatibility {
-#   dir=$1
-#   output=$(
-#     python buildscripts/idl/idl_check_compatibility.py -v \
-#       --old-include "$dir/src" \
-#       --old-include "$dir/src/mongo/db/modules/enterprise/src" \
-#       --new-include src \
-#       --new-include src/mongo/db/modules/enterprise/src \
-#       "$dir/src" src
-#   )
-#   exit_code=$?
-#   echo "Performing idl check compatibility with release: $dir:"
-#   echo "$output"
-#   if [ $exit_code -ne 0 ]; then
-#     exit 255
-#   fi
-# }
-# export -f run_idl_check_compatibility
-# find idls -maxdepth 1 -mindepth 1 -type d | xargs -n 1 -P 0 -I % bash -c 'run_idl_check_compatibility "$@"' _ %
-
-# # Run the idl compatibility checker script with the current src directory as both the "old" and
-# # "new" versions. This is so that we can check that commands that were newly added since the last
-# # release adhere to compatibility requirements.
-# echo "Performing idl check compatibility for newly added commands since the last release:"
-# $python buildscripts/idl/idl_check_compatibility.py -v --old-include src --old-include src/mongo/db/modules/enterprise/src --new-include src --new-include src/mongo/db/modules/enterprise/src src src
+# Run the idl compatibility checker script with the current src directory as both the "old" and
+# "new" versions. This is so that we can check that commands that were newly added since the last
+# release adhere to compatibility requirements.
+echo "Performing idl check compatibility for newly added commands since the last release:"
+$python buildscripts/idl/idl_check_compatibility.py -v --old-include src --old-include src/mongo/db/modules/enterprise/src --new-include src --new-include src/mongo/db/modules/enterprise/src src src