Make the cookies: Whisk the flour, cocoa powder, baking soda, and salt together in a large mixing bowl. Set aside.
Add the chocolate chips and milk to a microwave-safe bowl. Microwave in 15 second increments, stirring in between until melted. It should only take about 15-30 seconds total. Set aside to allow to cool.
Using a handheld or stand mixer with the paddle attachment, beat the butter on high speed until creamy, about 1 minute. Scrape down the sides and bottom of the bowl as needed. Reduce the mixer to medium speed and add the brown sugar until combined. Beat in the eggs and vanilla extract, scraping down the sides and bottom of the bowl as needed. With the mixer on low speed, slowly add the dry ingredients. I find it's easiest to use a 1/4 cup dry measuring cup or spoon for this. Add in the melted chocolate and beat until just combined. The dough will be very sticky. Cover the dough tightly, or place in an airtight container and chill for at least 2 hours. Chilling is required.
Remove the cookie dough from the refrigerator and allow to sit at room temperature for 5 minutes. If refrigerated for more than 4 hours, let it sit at room temperature for 15 minutes. Preheat the oven to 350°F. Line two large baking sheets with parchment paper or silicone baking mats (preferred). Set aside.
Scoop 1 Tablespoon of dough, form into a ball, and roll in the pecans. Repeat for each cookie. Place 8-10 balls onto each baking sheet. Bake for 10-11 minutes. Remove from the oven and allow to cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.
Make the caramel: In a medium sauce pan over medium-high heat, melt the better. Once the butter is melted, add the brown sugar and whisk continuously until the sugar is completely dissolved.
Whisk in the heavy cream and bring to a boil for 2-3 minutes. Remove from the heat and whisk in the vanilla extract. The mixture will bubble up a bit due to the temperature difference. Allow the caramel to cool before storing in a jar.
Drizzle warm caramel over the cookies and allow to set for at least 10-15 minutes.
Store cookies at room temperature for up to 5 days in an airtight container. The caramel stays fresh in the refrigerator for up to 2 weeks.
Make ahead tip: Cookies (without caramel) can be frozen for up to 3 months. Unbaked, unrolled cookie dough balls can be frozen for up to 3 months. Let them sit at room temperature for 15 minutes, pre-heat the oven, then roll in chopped pecans. The caramel can be made up to 2 weeks in advance. Warm the caramel up for a few seconds in the microwave before using.1Any milk fat % can be used. I typically use 1% or 2%.2Heavy cream or half-and-half work best for producing the best tasting caramel. Whole milk may work but I can guarantee results.