Preheat oven to 350 F. Place half of the pretzels onto a baking sheet. Place one mini Reese's peanut butter cup onto each pretzel.
Bake for 3-4 minutes. Remove from oven, sandwich each with the remaining pretzels. Place chocolate chips into a microwave-safe bowl. Heat in the microwave in 30 second intervals, stirring after each until fully melted and smooth.
Dip half of each pretzel into the melted chocolate. Place onto a plate, refrigerate until the chocolate has set.