Cook the pasta according to package directions. Drain and set aside.
In a large, heavy-bottomed pot, melt the butter over medium heat. Add the flour and whisk, forming a roux.
While whisking continuously, slowly add the milk.
Add the pumpkin puree, cinnamon, nutmeg, and thyme. Whisk to combine.
Allow this pumpkin-y sauce to cook for a few minutes, whisking occasionally. It will thicken slightly.
To the sauce, add the cheese, whisking to combine. Add salt and pepper to taste.
Add the cooked pasta to the cheese sauce, and eat!