Preheat oven to 250 degrees F. Line a rimmed baking sheet with aluminum foil.
Pour popcorn into a large bowl and set aside.
Melt butter in a large pot over medium-high heat. Add the brown sugar and corn syrup and bring mixture to a boil, stirring constantly so that it doesn’t burn. Reduce the heat to low and simmer for 5 minutes. Whisk in salt, baking soda and vanilla.
Pour caramel sauce over the popcorn and toss until it is evenly coated with the caramel.
Spread the mixture onto the prepared baking sheet or pan in an even layer. Sprinkle with flaky sea salt. Bake for about 1 hour, stirring to toss every 15 minutes, until the popcorn is a deep golden color. (Baking is key to crunchy caramel corn.)
Remove the pan from the oven and let cool to room temperature. Break up the caramel corn with your hands or a wooden spoon. Store in an airtight container for up to a week.