Note: This is not Flipnote Studio 3D. This is Flipnote Studio, which was free on the DSi Shop. You can get Flipnote Studio 3D from Nintendo.
To install, you'll need to set up custom firmware on your 2DS/3DS/New 3DS first. The guide at 3ds.guide will always be up to date.
These are in the .CIA (CTR Installable Archive) format for 3DS - plunk on your SD card and install with the FBI app, which will be installed while you follow the guide linked above.
Make sure to pick the correct version for your system region, or it won't work.
Also included are downloads for Nintendo DSi Camera and Sound, which can be used in tandem with Flipnote Studio.
If you live in South or North America, this is the one for you.
Vives en Sudamรฉrica? Usa este.
Flipnote Studio: 0c063e8ccba4d70002b8b8d298f3eab0 DSi Camera: d27f371ea4723af10625f6750ee89a74 DSi Sound: a03bf52ba33d495a3666a521917e3453
If you don't live in the Americas or Japan, use this one.
Nintendo DSi Camera (not yet available)
Nintendo DSi Sound (not yet available)
Flipnote Studio: 5c61b3af9608f63240c25a34f64580a6 DSi Camera: file not available DSi Sound: file not available
Nintendo DSi Camera (not yet available)
Nintendo DSi Sound (not yet available)
Flipnote Studio: 4a8e7904512086e5148996086e9d5da1 DSi Camera: file not available DSi Sound: file not available