Coat an 8x8-inch baking dish with cooking spray and set aside.
Bring a large pot of lightly salted water to a boil. Cook whole wheat macaroni in the boiling water, stirring occasionally, until tender yet firm to the bite, about 8 minutes.
Set an oven rack about 6 inches from the heat source and preheat the oven's broiler.
Stir 1 tablespoon evaporated milk and tapioca together in a saucepan. Whisk in remaining milk. Stir in Cheddar cheese, mustard, Worcestershire sauce, and pepper. Bring to a simmer and stir until the sauce thickens a bit and cheese is completely melted. Drain pasta and stir into the sauce. Spoon into the prepared baking dish.
Cook under the broiler until top browns, 2 to 3 minutes. Remove from oven and allow to cool for 5 minutes before serving.