Stir flour, oats, brown sugar, and cinnamon together in a bowl. Pour melted butter into oat mixture and stir until crumbly. Pat half the oat mixture into the bottom of a 9x13-inch baking dish.
Stir rhubarb and apples together in a bowl; pour on top of oat mixture in baking dish.
Stir cornstarch and 2 tablespoons water together in a bowl until cornstarch is dissolved and mixture is smooth.
Heat sugar, 1 cup water, and vanilla extract in a saucepan over medium-high heat; bring to a boil, stirring constantly. Pour cornstarch mixture into sugar mixture and continue to boil, stirring constantly, until mixture thickens, 1 to 2 minutes. Drizzle sugar mixture over rhubarb and apples; sprinkle remaining oat mixture over the top.
Bake in the preheated oven until hot and bubbly, 35 minutes.