Heat the oven to 425F. Butter a 9x13" dish or spray with nonstick cooking spray.
Bring a large pot of salted water to a boil. Cook pasta according to the direction package. Drain.
Melt butter in a large pot over medium heat. Add the flour, cook, whisking constantly until the butter smells fragrant and nutty.
Slowly pour in the milk and flour. Continue whisking until the sauce bubbles and thickens.
Add the cheese and pumpkin puree. Stir until the cheese has melted and the sauce is smooth. Taste the sauce and adjust with cayenne pepper, salt and pepper.
Add in pasta and mix well. Transfer to a baking dish.
Topping: melt the butter and combine with panko and thyme leaves. Sprinkle over mac and cheese.
Bake in the oven for 10-15 minutes or until golden brown on top.