Brown the butter: Melt the butter in a light-colored saucepan over medium heat, swirling often, until it turns golden amber and smells nutty, about 5 to 7 minutes. Pour it into a heatproof bowl immediately to stop the cooking.
Cool slightly: Let the brown butter sit for about 5 minutes so it's warm but not hot. This keeps it from cooking the egg yolk when combined.
Mix wet ingredients: Whisk the brown butter with brown sugar, granulated sugar, pumpkin puree, egg yolk and vanilla extract until smooth and glossy, about 1 minute.
Whisk dry ingredients: In a separate bowl, whisk together the flour, pumpkin pie spice, baking soda and salt until evenly combined.
Combine wet and dry: Add the dry ingredients to the wet mixture and stir just until no flour streaks remain. The dough will be thick.
Fold in chocolate chips: Gently fold in the chocolate chips, mixing just enough to distribute them evenly without overworking the dough.
Chill the dough: Cover the bowl and refrigerate the dough for at least 30 minutes. This firms up the butter so the cookies hold their shape in the oven.
Preheat the oven: While the dough chills, preheat the oven to 350°F and line two baking sheets with parchment paper.
Scoop the dough: Scoop the chilled dough into 1.5-tablespoon mounds and place them about 2 inches apart on the prepared baking sheets.
Bake the cookies: Bake for 10 to 12 minutes, until the edges look set and lightly golden but the centers still look slightly soft and underbaked.
Cool on the sheet: Let the cookies cool on the baking sheet for 5 minutes so they finish setting, then transfer to a wire rack to cool completely.