Preheat oven to 350 degrees F. Line two baking sheets with parchment paper.
In a medium bowl, whisk together the flour, cocoa powder, chile powder, baking soda and salt. Set aside.
In the bowl of a stand mixer fitted with the paddle attachment, beat the butter on medium-high speed until light and creamy, about 1 minute. Add the brown and granulated sugar and beat until slightly fluffy, about 2 minutes, scraping down the sides of the bowl with a rubber spatula as needed. Add the egg and vanilla and beat until well combined.
Reduce the mixer speed to medium-low, add half the flour mixture, and beat until just combined, then add the remaining flour mixture and beat until the mixture just comes together, 1 to 2 minutes, being careful not to overmix. Add the chocolate chunks and pepitas and beat on low until just combined.
Use a 2-ounce ice cream scoop or a 1/4 cup measuring cup to scoop the cookie dough onto the prepared baking sheets, making about 14 cookies total and leaving at least 2 inches between each cookie.
Bake until the edges of the cookies are crisp but the centers are still tender, about 15 minutes, rotating the baking sheets top to bottom and front to back halfway through the baking time. Remove from the oven, set the baking sheets on wire racks, and let the cookies cool completely on the pans. They should keep up to 5 days in an airtight container.