Before you begin, please note that this requires an original 3DS or 3DS XL, the n3DS will not work. Secondly, this requires a firmware version on or before 9.5.0-22. And finally, you will already need to own a GBC game. That includes games from the ambassador program. There will be a list of required materials at the bottom.

To begin, you will need to remove the SD card from your 3DS, and insert it into your computer. Next, you will need to download GBCRomSwap from the link at the bottom of the post, and copy the file code.bin to the root of your SD card(that means its not in a folder, its directly on the sd card). You will also need to copy a GBC rom, with the filename “rom.gbc” (without the quotes, also into the root of the sd card).

Next, you’ll have to put the SD card back into your 3ds, and turn it on. Open a Virtual console Gameboy Color game, and open the virtual console menu (Tapping the touch screen). Reset the game (You will lose your save data, so make sure to use a game you don’t care about) and push home. Open the browser, and go to http://loadcode.projectpokemon.org . Your ds will pause and hang for a moment, and you will see a color on the touch screen. Red means the VC ROM was not found in the RAM. Yellow means the ROM you were injecting is too large, either try a smaller ROM or a VC game with a bigger ROM. Finally, Green means it was successful.

Go back into the game after your 3DS crashes back to the home menu with an error, and reopen your VC game. Open the VC menu, and touch reset once more. When it resets, it should load the GBC game!

This process can also be done with Gameboy (Not advance) games! Just make sure to use a VC Gameboy game as the base for your ROM.

gbc

Requirements:
◾Original 3DS/3DS XL
◾Firmware 9.5.0-22 or lower
◾SD Card with enough space for the ROM and exploit file
◾Computer with working internet connection & a way to transfer files to the SD card
◾VC Game from the eShop, GBC for a GBC ROM, or GB for a GB ROM.
◾A GB or GBC ROM to load

http://wololo.net/2015/04/28/how-to-...c-roms-on-3ds/