Note:

Alternatively, starting Nintendo eShop on a Nintendo 3DS system that is displaying Pokémon X or Pokémon Y on the HOME Menu will prompt a notification, from which you can open Nintendo eShop and download the update data.

For detailed information on how to connect to the internet, click here.

2.

Select the Pokémon X: Update or Pokémon Y: Update and download it. Once the download is complete, the update will automatically be applied.