In a medium saucepan, whisk together the brown sugar, cornstarch, cinnamon, nutmeg, and salt until well combined and no lumps remain.
Whisk in the apple cider and apple cider vinegar.
Bring the mixture to a boil over medium heat, stirring often. Once bubbling, cook for 4 to 5 minutes, stirring, until the syrup looks glossy and coats the back of a spoon. It will still look slightly thin at this point.*
Remove from the heat. Stir in the butter until melted, then stir in the vanilla.
Serve warm over apple cider pancakes or your favorite breakfast treats.
Notes
*The syrup will thicken as it sits and cools, so don't worry if it seems a little thin while it is still hot.