In a saucepan over medium heat, combine fresh cranberries, honey, sugar, and lemon juice. Stir occasionally until the mixture starts to bubble and the cranberries pop (about 5-7 minutes). Remove from heat and let it cool slightly.
Roll out the thawed puff pastry on a lightly floured surface and cut it into squares, approximately 3x3 inches. You should get about 12 squares from one sheet.
Place the puff pastry squares into a greased mini muffin tin, pressing them gently into the cups.
Add a small cube of Brie cheese to each pastry cup.
Spoon a teaspoon of the cranberry mixture over the Brie in each cup.
Brush the edges of the puff pastry with the beaten egg for a golden finish.
Bake in the preheated oven for 15-20 minutes or until the pastry is puffed and golden brown.
Allow to cool for a few minutes before carefully removing from the muffin tin.
Garnish each bite with fresh thyme leaves and a sprinkle of cracked black pepper if desired.