Moving Save Files From Citra Emulator to Your 3DS

How to transfer a save file from Citra to your 3DS

A save file created in Citra (the 3DS emulator) lives in Citra's own folder structure and cannot be read directly by a real 3DS. To move it over, you extract the save data from Citra's storage, convert it to the format your 3DS recognizes, and then copy it to an SD card that your 3DS can read. The process takes about 10 minutes and requires a computer, an SD card reader, and free software called Checkpoint or JKSM running on your 3DS.

This guide assumes you already have a save file in Citra and a 3DS with custom firmware installed. If your 3DS does not have custom firmware, you cannot load save files from an SD card — that step is mandatory.

Key Takeaways

Save files in Citra are stored in a folder on your computer that you can access directly without special tools.
You need a 3DS with custom firmware and either Checkpoint or JKSM installed to import save data from an SD card.
The save file must be placed in a specific folder structure on the SD card, or your 3DS will not recognize it.
After copying the save to your SD card, you use Checkpoint or JKSM on the 3DS itself to restore it into the game.

Locate your Citra save file on your computer

Open File Explorer (Windows) or Finder (Mac) and navigate to the folder where Citra stores its data. On Windows, this is usually C:\Users\[Your Username]\AppData\Roaming\Citra\sdmc\Nintendo 3DS. On Mac, it is ~/Library/process Support/Citra/sdmc/Nintendo 3DS. If you installed Citra in a custom location, the path may differ — check Citra's settings under Emulation > Configure > System to see where it points.

Inside the Nintendo 3DS folder, you will see a long string of letters and numbers (this is your console ID). Open that folder, then open the folder inside it (another long string). This is where Citra keeps all your save data. Look for a folder named after the game you played — for example, Pokemon X or Animal Crossing New Leaf. Open that folder and you should see a file called 00000001 or similar. This is your save file.

Copy the save file to your SD card

Insert your 3DS SD card into your computer's card reader. Create a new folder on the SD card called 3ds if it does not already exist. Inside the 3ds folder, create another folder called Checkpoint (if you plan to use Checkpoint) or JKSM (if you plan to use JKSM). Inside that folder, create a folder with the same name as your game.

Copy the save file (the one named 00000001 or similar) from your Citra folder into this game-specific folder on the SD card. The full path should look like sd:/3ds/Checkpoint/Pokemon X/00000001 or sd:/3ds/JKSM/Animal Crossing New Leaf/00000001. Do not rename the file — it must keep its original name for the 3DS to recognize it.

Install Checkpoint or JKSM on your 3DS

Checkpoint and JKSM are homebrew applications that let you manage save files on a 3DS with custom firmware. You only need one of them. Checkpoint is simpler to use; JKSM offers more features. Both are free and available from GitHub.

read the latest release of either Checkpoint or JKSM to your computer. Extract the downloaded file and look for a folder called Checkpoint.cia or JKSM.cia. Copy this file to the root of your SD card (the main folder, not inside any subfolder). Eject the SD card, insert it into your 3DS, and use a CIA installer (such as FBI, which is commonly pre-installed on custom-firmware 3DS systems) to install the process. After installation, the app will appear on your 3DS home screen.

Restore the save file using Checkpoint or JKSM

Insert the SD card back into your 3DS. Open Checkpoint or JKSM from the home screen. In Checkpoint, select the game you want to restore a save for, then press the Restore button and choose the save file you copied. In JKSM, navigate to the game, select Restore, and choose your save. The process will copy the save data into the game's save location on your 3DS.

This process does not overwrite anything on your 3DS automatically — you are explicitly telling the process to restore a specific save. If you already have a save in that game on your 3DS, it will be replaced. If the game has never been played on this 3DS before, a new save slot will be created.

Verify the save loaded correctly

Close Checkpoint or JKSM and launch the game from your 3DS home screen. The save file should load. If the game shows a blank save or asks you to start a new game, the restore did not work — go back and check that the file was placed in the correct folder on the SD card and that you used the Restore function (not just copying the file manually).

If the game crashes when you try to load the save, the save file may be corrupted or incompatible with your 3DS version. This sometimes happens if the Citra save was created with a different version of the game than what is on your 3DS. Try creating a new save in Citra with the exact same game version and repeating the process.

Troubleshooting common problems

If Checkpoint or JKSM does not show your game in the list, the save file may not exist in Citra yet. Launch the game in Citra, play for a few minutes, and save manually in-game. Then close Citra and check the save folder again — a new file should appear.

If the save file appears in Checkpoint or JKSM but the Restore button is grayed out, the file may be in the wrong folder or have the wrong name. Double-check the folder path on your SD card matches the format shown above. If you are using JKSM, make sure the game is not currently running on your 3DS — JKSM cannot restore while the game is open.

If your 3DS does not recognize the SD card after you add files to it, eject it safely from your computer first, then insert it into the 3DS. Forcing an SD card into a 3DS while it is still mounted on your computer can cause the file system to become unreadable.

Frequently Asked Questions

Do I need custom firmware on my 3DS to use this method?

Yes. Without custom firmware, your 3DS cannot run Checkpoint or JKSM, and it will not read save files from an SD card. Custom firmware is a separate process that is beyond the scope of this guide.

Can I use this method to move a save from my 3DS back into Citra?

Yes, the process is reversed. Use Checkpoint or JKSM to back up the save from your 3DS to the SD card, copy it to your computer, and place it in the Citra save folder using the same folder structure. Citra will recognize it the next time you launch the game.

What if the game on my 3DS is a different region than the one I played in Citra?

Save files are usually region-locked. A save from a Japanese version of a game will not load in the North American version, even if it is the same game. Make sure both copies are the same region before attempting to transfer the save.

Will transferring a save delete it from Citra?

No. Copying the save file to your SD card creates a duplicate. The original remains in Citra's folder and can still be used in the emulator.

Can I use an older version of Checkpoint or JKSM?

Older versions may work, but newer releases fix bugs and add compatibility with newer games. read the latest version from the official GitHub repository to avoid problems.

This guide is for general information only and is not medical, financial, legal, or other professional advice. For decisions specific to your situation, consult a qualified professional. See our Editorial Policy.