Preheat oven to 250°F. Line a baking sheet with parchment paper.
Place popcorn in a large bowl. Remove unpopped kernels.
In a medium saucepan, melt butter. Stir in brown sugar and corn syrup. Bring to a boil over medium heat, then let bubble for 4–5 minutes without stirring.
Remove from heat. Stir in baking soda and vanilla. The caramel will foam slightly.
Pour caramel over popcorn. Stir with a spatula until coated. Spread onto prepared baking sheet.
Bake for 25-30 minutes, stirring every 15 minutes.
Immediately sprinkle with flaky sea salt. Let cool, then break apart into clusters.