Preheat oven to 350°F (175°C) and line two 24-cup mini muffin tins with paper liners.
In a large mixing bowl, whisk together the flour, sugar, cocoa powder, baking soda, and salt until well combined.
Make a well in the center of the dry ingredients and pour in the water, oil, vinegar, and vanilla extract.
Whisk the mixture starting from the center and moving outward until the batter is smooth and free of large lumps.
Distribute the batter into the prepared mini muffin liners, filling each approximately two-thirds full.
Bake for 12 to 15 minutes, or until a wooden skewer inserted into the center of a cupcake comes out clean.
Remove the tins from the oven and allow the cupcakes to cool in the pan for 5 minutes.
Transfer the cupcakes to a wire cooling rack to cool completely before frosting or serving.