Hmz, I seem to have found the solution...
Silly that I overlooked it: https://github.com/tymondesigns/jwt-auth/wiki/Authentication
Note to Apache users
Apache seems to discard the Authorization header if it is not a base64 encoded user/pass combo. So to fix this you can add the following to your apache config
RewriteEngine On
RewriteCond %{HTTP:Authorization} ^(.*)
RewriteRule .* - [e=HTTP_AUTHORIZATION:%1]
Alternatively you can include the token via a query string
http://api.mysite.com/me?token={yourtokenhere}
I started using ?token={my_token} and now all works fine..