Preheat your oven to 350°F. Line a 12-cup muffin tin with paper liners and set aside.
Make the Cupcake Batter
In a large bowl or stand mixer, combine cake mix, water, oil, and eggs. Mix on low until just combined, then bump to medium speed and mix 2–3 minutes more until smooth.
Bake
Spoon batter into liners, filling each about ½ to ⅔ full. Bake 14–16 minutes, until the edges turn light golden and a toothpick comes out clean. Cool completely before filling.
Whisk the Filling
In a bowl, whisk together vanilla pudding mix and cold milk for about 2 minutes. Chill until you’re ready to use it.
Make the Ganache
Place chocolate chips and heavy cream in a microwave-safe bowl. Microwave 30 seconds, stir, then microwave another 30 seconds. Stir until smooth and glossy. Let cool to room temperature.
Core & Fill
Use a cupcake corer or teaspoon to scoop a small hole from the top of each cupcake. Save the little cake pieces. Pipe or spoon pudding filling into each cupcake until level, then press the reserved cake piece back on top.
Dip in Ganache
Carefully invert each filled cupcake and dip just the top into the ganache. Place ganache side up on a wire rack and let set.
Notes
Can I use homemade pastry cream instead of pudding mix? Yes! Homemade pastry cream makes a richer vanilla cream filling but takes a bit more time.How long do Boston Cream Pie Cupcakes last? Store in an airtight container in the fridge for up to 3 days. Let them come to room temperature before serving for best flavor.Why did my ganache break? If your ganache looks grainy or separated, it may have overheated. Stir gently off heat and let it cool slowly before dipping.