Preheat oven to 325 degrees F.
In a medium bowl, combine the flour, baking soda, and salt. Whisk until ingredients are well combined, then set aside. In the bowl of a stand mixer with the paddle attachment, add the butter, sugar, brown sugar, and vanilla and cream together until light and fluffy—about 3-4 minutes. Add eggs one at a time, mixing them in after each addition and scraping down the sides as needed.
Add the flour mixture to the butter mixture and mix on low until just combined, then add chocolate chips and 1/2 of the Reese's Peanut Butter Cups pieces. Mix gently by hand using a rubber spatula, making sure to scrape the bottoms and sides of the bowl and combine all ingredients well.
Using a small ice cream scoop, or a spoon, scoop and roll dough into 1¼" balls. Place them 2" apart on a baking sheet lined with parchment paper, then use the palm of your hand to press the balls down so the dough ball is about 3/4" thick.
Bake for 10-12 minutes, or until the edges begin to turn lightly golden brown. Once baked, remove from the oven and sprinkle the reserved Reese's Peanut Butter Cups on top of the cookies.
Let the cookies cool on the baking sheet for a couple minutes before moving them to a wire rack to cool completely. Enjoy!