Preheat the oven to 375 degrees and grease a 12-cup muffin tin.
Cook the elbow macaroni in a large pot of boiling water until al dente, then drain and set aside.
In a saucepan, melt the butter over medium heat. Whisk in the flour and cook for one minute.
Slowly whisk in the milk until smooth, then stir in the pumpkin puree, salt, and pepper. Cook until the sauce thickens slightly.
Remove the sauce from heat and stir in the shredded cheddar cheese until melted.
In a large bowl, beat the eggs, then mix in the cooked macaroni and cheese sauce until everything is coated.
Spoon the mixture evenly into the prepared muffin tin, filling each cup to the top. Sprinkle panko breadcrumbs over each bite.
Bake for 20 to 25 minutes until the tops are golden and the bites feel set. Cool for five minutes before removing from the tin.