Assuming you are using Luma3DS. Then you'll need to use Luma3DS' payload chainloading feature.
Link:
https://github.com/AuroraWright/Luma3DS/wiki/Other-features-and-notes#payload-chainloading
Basically download the latest release of Decrypt9WIP.
Link:
https://github.com/d0k3/Decrypt9WIP/releases
1. Copy Decrypt9WIP.bin from the Decrypt9WIP zip to the /luma/payloads/ folder on your SD card.
2. In the /luma/payloads folder, rename Decrypt9WIP.bin to down_Dec9.bin
Now hold the D-PAD Down, and you'll boot into Decrypt9 at boot time. You can change the button to whatever you want, as long as it's a valid one as described in the Luma3DS wiki that I linked above.
Basically why we can't load Decrypt9 from the Homebrew Launcher is because we need arm9 privileges.