Despite cloud saving being a pretty common feature nowadays and even the PSVita supporting it with PS Plus, Nintendo decided to leave the 3DS out of the party and as a result, you need to backup Checkpoint saves manually by reading them from the SDCard.
Despite the 3DS being from the same generation of the PSVita, Nintendo didnít give it cloud saving support but the homebrew community is here to fix that! (Image Source)

Now, things on this front have started to change thanks to Kyraminolís 3DSync despite the console almost 9 years old.
As its name may suggest, 3DSync is a homebrew utility letting you upload Checkpoint save games to Dropbox although itís in early stages at this point. Using it is pretty simple as it only requires you to:

  • Install the CIA or a run a 3DSX fil
  • Use this configurator website to generate settings in order to use the Dropbox API
    • This generates a Ď3DSync.inií file which you should put in /3ds/3DSync/3DSync.ini on your SDCard

  • Backup save games with Checkpoint
  • Open 3DSync and have your saves uploaded to the cloud!

Its developer currently plans to add support for more platforms including more cloud services, a local PC client and the ability to transfer saves wirelessly between different 3DS consoles.
You may read more about 3DSync and find its download links from its GBATemp thread.