Puree the diced watermelon in a blender until smooth. Strain the puree through a fine mesh sieve to remove excess pulp and seeds, then measure out 1 cup of the strained juice.
In a large mixing bowl, combine the flour, baking powder, and salt. Whisk together until evenly distributed.
In a separate bowl, beat the eggs with the sugar until the mixture is light and slightly frothy, about 2 minutes. Add the melted butter, vanilla extract, and watermelon puree, then blend until smooth.
Gradually add the wet mixture to the dry ingredients, alternating with the milk, beginning and ending with the dry ingredients. Use a silicone spatula to fold gently until just combined; do not overmix.
Line a cupcake tin with paper liners and evenly distribute the batter among the cups, filling each about two-thirds full. Bake in a preheated oven at 350°F (180°C) for 20-25 minutes, or until a toothpick inserted into the center comes out clean.
Remove the cupcakes from the oven and allow them to cool in the tin for 5 minutes. Then transfer to a wire rack and cool completely before frosting or serving. The cupcakes will have a light golden top and a moist, tender crumb inside.
