Preheat the oven to 350 F. Line a 12 cup muffin pan with paper liners. In a medium bowl, whisk together flour, salt, and baking soda. In a large bowl, mix together butter, brown sugar, and granulated sugar until fluffy.
Add in the egg and vanilla extract, and mix until smooth. Add in the flour mixture, mix until it is fully combined. Fold in the chocolate chips. Evenly divide the cookie dough between the prepared muffin pan.
Bake for 12-15 minutes. Remove from the oven, and top each cookie cup with a peanut butter cup.