Debian testing or unstable

Debian unstable and testing are usually fairly up to date, so this should be enough:

sudo apt install git-annex

Debian 9.0 "stretch"

Debian's stable release contains git-annex version 6.20170101.

sudo apt install git-annex

A newer version of git-annex is available in backports.

Standalone backports for all releases

If the version shipped with Debian is too old, the NeuroDebian team provides a standalone build package that is regularly updated and that should work across all releases of Debian.