Preheat oven to 350°F (175°C). Line two baking sheets with parchment paper and set aside.
In the bowl of a stand mixer with a paddle attachment (or using a hand-held mixer), beat the softened butter, brown sugar, and honey together until the mixture is smooth, glossy, and fully combined.
Add the egg and beat until incorporated. Mix in the vanilla extract.
In a separate medium bowl, whisk together the flour, baking soda, and salt.
Add the dry ingredients to the wet ingredients. Mix on low speed just until combined; do not overmix. The dough should be soft but not sticky.
Gently fold in the chocolate chunks.
Scoop the dough into 2-tablespoon portions and place them 2 to 3 inches apart on the prepared baking sheets.
Bake for 8 to 10 minutes, or until the edges are lightly golden and set, but the centers still look slightly underbaked.
Remove the cookies from the oven and immediately sprinkle each one with a pinch of flaky sea salt.
Allow the cookies to cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.
Store in an airtight container at room temperature for up to 4 days.