Unity's been exporting to all the major consoles for some time now, and has added the New Nintendo 3DS to their list of supported consoles (if the New/Old Nintendo 2/3DS naming confuses you, or you're having a hard time keeping up, give this Wikipedia article a good look). Following up from last year's announcement, Unity has released a special build available to registered Nintendo developers.
If you're not yet a Nintendo developer and want to get into the program, you can sign up at Nintendo's Developer Portal. The Unity for Nintendo 3DS program is the same price as Unity (in other words, it's free) for all developers, so entry into the program is pretty simple. We hope to see many developers bring their dreams to reality on the New Nintendo 3DS with Unity!