diff --git a/Gemfile b/Gemfile
index 69d793e7e7..a151034f03 100644
--- a/Gemfile
+++ b/Gemfile
@@ -25,3 +25,5 @@ gem 'i18n', *i18n_versions
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem
 gem "tzinfo-data", platforms: %i[ windows jruby ]
+
+gem 'ostruct' if RUBY_VERSION >= '4.0'
diff --git a/lib/mongoid/config.rb b/lib/mongoid/config.rb
index 98ae824d1b..4df6129d90 100644
--- a/lib/mongoid/config.rb
+++ b/lib/mongoid/config.rb
@@ -294,6 +294,15 @@ def validate_isolation_level!(level)
     # See https://jira.mongodb.org/browse/MONGOID-5892 for more details.
     option :serializable_hash_with_legacy_only, default: true
 
+    # When true (default), all top-level query operators are passed through
+    # to MongoDB without restriction when using +where+/+find_by+. Set to
+    # false to enable a strict allowlist that rejects operators like +$where+
+    # and +$function+, which can execute arbitrary JavaScript when user-supplied
+    # input reaches the query builder.
+    #
+    # See https://jira.mongodb.org/browse/MONGOID-5939 for details.
+    option :allow_unsafe_query_operators, default: true
+
     # Returns the Config singleton, for use in the configure DSL.
     #
     # @return [ self ] The Config singleton.
diff --git a/lib/mongoid/criteria/queryable/selectable.rb b/lib/mongoid/criteria/queryable/selectable.rb
index 8317c9befd..41035a4c8d 100644
--- a/lib/mongoid/criteria/queryable/selectable.rb
+++ b/lib/mongoid/criteria/queryable/selectable.rb
@@ -792,6 +792,13 @@ def where(*criteria)
         #
         # @return [ Selectable ] The cloned selectable.
         # @api private
+        # Operators permitted in a query expression without opt-in.
+        # Excludes $where (JS execution) and other operators not needed for
+        # ordinary application queries.
+        ALLOWED_QUERY_OPERATORS = %w[
+          $and $or $nor $not $text $comment $expr $jsonSchema $alwaysFalse $alwaysTrue
+        ].freeze
+
         def expr_query(criterion)
           raise ArgumentError, 'Criterion cannot be nil here' if criterion.nil?
           unless criterion.is_a?(Hash)
@@ -803,7 +810,11 @@ def expr_query(criterion)
             normalized.each do |field, value|
               field_s = field.to_s
               if field_s.start_with?('$')
-                # Query expression-level operator, like $and or $where
+                unless Mongoid.allow_unsafe_query_operators? || ALLOWED_QUERY_OPERATORS.include?(field_s)
+                  raise Errors::InvalidQuery,
+                    "Operator '#{field_s}' is not allowed in a query expression. " \
+                    "Set Mongoid.allow_unsafe_query_operators = true to permit all operators."
+                end
                 query.add_operator_expression(field_s, value)
               else
                 query.add_field_expression(field, value)
diff --git a/spec/mongoid/criteria/queryable/selectable_spec.rb b/spec/mongoid/criteria/queryable/selectable_spec.rb
index ae142711c4..4f240493ce 100644
--- a/spec/mongoid/criteria/queryable/selectable_spec.rb
+++ b/spec/mongoid/criteria/queryable/selectable_spec.rb
@@ -2163,4 +2163,5 @@ def localized?
       end
     end
   end
+
 end
diff --git a/spec/mongoid/criteria/queryable/selectable_where_spec.rb b/spec/mongoid/criteria/queryable/selectable_where_spec.rb
index f066f037bd..39c6752652 100644
--- a/spec/mongoid/criteria/queryable/selectable_where_spec.rb
+++ b/spec/mongoid/criteria/queryable/selectable_where_spec.rb
@@ -550,4 +550,67 @@ def self.evolve(object)
       end
     end
   end
+
+  describe "top-level operator injection guard" do
+    context "when allow_unsafe_query_operators is true (default)" do
+      context "when passing $where" do
+        it "does not raise" do
+          expect {
+            query.where('$where' => 'this.name == "admin"')
+          }.not_to raise_error
+        end
+      end
+
+      context "when passing $function" do
+        it "does not raise" do
+          expect {
+            query.where('$function' => { body: 'function() { return true; }', args: [], lang: 'js' })
+          }.not_to raise_error
+        end
+      end
+    end
+
+    context "when allow_unsafe_query_operators is false" do
+      config_override :allow_unsafe_query_operators, false
+
+      context "when passing $where" do
+        it "raises InvalidQuery" do
+          expect {
+            query.where('$where' => 'this.name == "admin"')
+          }.to raise_error(Mongoid::Errors::InvalidQuery, /\$where/)
+        end
+      end
+
+      context "when passing $function" do
+        it "raises InvalidQuery" do
+          expect {
+            query.where('$function' => { body: 'function() { return true; }', args: [], lang: 'js' })
+          }.to raise_error(Mongoid::Errors::InvalidQuery, /\$function/)
+        end
+      end
+
+      context "when the error mentions allow_unsafe_query_operators" do
+        it "includes the config opt-in in the message" do
+          expect {
+            query.where('$where' => 'true')
+          }.to raise_error(Mongoid::Errors::InvalidQuery, /allow_unsafe_query_operators/)
+        end
+      end
+
+      %w[$and $or $nor $not $text $comment $expr $jsonSchema $alwaysFalse $alwaysTrue].each do |op|
+        context "when passing #{op} (allowlisted)" do
+          it "does not raise" do
+            value = case op
+            when '$and', '$or', '$nor', '$not' then [{ 'x' => 1 }]
+            when '$text' then { '$search' => 'hi' }
+            when '$expr' then { '$gt' => ['$a', 1] }
+            when '$jsonSchema' then { 'required' => ['x'] }
+            else true
+            end
+            expect { query.where(op => value) }.not_to raise_error
+          end
+        end
+      end
+    end
+  end
 end