Prep your cookie sheet with parchment paper, and preheat your oven to 350 degrees Fahrenheit.
Dry out the pumpkin puree. How? By placing it in a paper towel and gently squeezing out the excess liquid. Again, we're trying to make pumpkin cookies, not bite-sized pumpkin cakes. We need to somewhat reduce the moisture content.
In a small saucepan over medium heat, melt the butter. Stir it regularly until the butter browns, making sure not to burn it.
Using a large bowl and a hand mixer (or the bowl of a stand mixer), add the brown butter and brown sugar. Whisk together. Keep in mind that we're using melted butter, so it's not going to produce the same texture as when you're creaming together softened butter and white granulated sugar.
Add in the egg yolks, one at a time, and the vanilla extract. Blend again, using a whisk or whisk attachment.
Add the dried-out pumpkin puree, and mix until well-combined.
In a separate bowl, whisk flour, pumpkin pie spice, baking soda, and salt. Slowly add the dry ingredients to the wet ingredients until a cookie dough forms.
Use a spoon to fold in the chocolate chunks, keeping some of the chunks back to place on top of each cookie.
Use a cookie scoop to make cookie dough balls, and place them on the parchment-lined baking sheets. Cover the baking sheets with plastic wrap and refrigerate for 30 minutes.
Top each cookie dough ball with a couple of chocolate chunks, then bake for 12-13 minutes or until the edges are slightly browned. The centers may look undone - don't worry! They'll finish cooking as they cool. It's the moisture from the pumpkin that's trying to fool you.
Let the cookies cool on the hot baking sheet for 10 minutes, then transfer them to a cooling rack to finish cooling.
Pour yourself a glass of milk and enjoy!