Preheat oven to 350 degrees F (175 degrees C). Butter 2-quart baking dish.
Place flour, 1/3 cup sugar, salt, and milk in mixing bowl. Whisk thoroughly to blend and break up any lumps. Whisk in eggs and vanilla until well blended. Ladle about half of the custard into the prepared baking dish.
Bake in preheated oven until set, about 12 minutes. Remove from oven. Distribute cherries evenly on top of the set custard. Sprinkle with 1/3 cup sugar. Ladle in the rest of the custard; avoid rearranging the cherries.
Bake until puffed and browned, about 45 minutes. Cool to just warm. Serve warm.