Preheat and cook pasta: Turn your oven to 375°F and get macaroni boiling—stop cooking 1 minute early so it stays firm, then drain it.
Make the roux: Melt ⅓ cup butter in your big pot over medium heat, then whisk in ⅓ cup flour little by little until smooth and bubbly.
Make cheese sauce base: Pour 3 cups milk in slowly while whisking nonstop, then cook about 5 minutes until it thickens up and just starts bubbling.
Add pumpkin mixture: Stir ¾ cup pumpkin, ¼ tsp nutmeg, ¼ teaspoon thyme, 1 tsp salt, and 1 tsp pepper in there until everything mixes together.
Melt cheese gradually: Toss in 4 ounces cheddar and 4 ounces Gruyere bit by bit, stirring each handful until it melts completely and your sauce gets silky.
Combine with pasta: Take the pot off heat, dump in your drained macaroni, and stir it all up so every noodle gets coated with that yummy sauce.
Prepare for baking: Scoop the whole thing into your 2-quart dish without greasing it, then sprinkle ⅓ cup panko over the top for that crunchy golden layer.
Bake until golden: Stick it in the oven for 25 minutes until the breadcrumbs turn brown and you see bubbles around the edges—then it's time to EAT!