Preheat oven to 350 degrees F.
Sift together flour, cocoa powder, baking soda, and salt. Set aside.
In the bowl of a stand mixer fitted with the paddle attachment, cream together butter, brown sugar, and granulated sugar until light and fluffy, 3-4 minutes.
Beat in vanilla and eggs, one at a time. Scrape the bowl.
Gradually add the flour mixture, mixing on low speed until combined. Scrape the bowl occasionally.
Mix in peanut butter chips by hand with a spatula or wooden spoon.
Scoop the dough into 24 portions onto parchment-lined baking sheets, spaced 2-inches apart.
Bake for 8-12 minutes, until the center is set, but still fudgy. For the best results, don't overbake.
Let cookies cool for 5-8 minutes on the baking sheets before transferring with a thin spatula to wire racks to cool completely.
If desired, press a few extra peanut butter chips into the tops of the cookies while they're warm for decoration.
Store at room temperature in an airtight container for up to 3 days.
