Yes, if you have API access. Please find the documentation here: Passwordless APIs
The process would go like this:
Call Start /api/passwordless/start, capture the code code.
Call Login /api/passwordless/login with code
Get a JWT and do with it what you normally would
For a Two Factor setup you would:
Call Start /api/two-factor/start consume code
Call Login /api/two-factor/login with code
Get a JWT
If the end user never needs to log themselves in, you may also consider:
Assign a random application password to a user.
Use that known password to call the Login API
Get a JWT!
Optionally remove the application password if you want it to be a one time use password.
This does have the issue of not creating an SSO session for the user, but that may not be a problem. (If someone logs in this way, and then goes to another application which has a login page managed by the 'hosted login pages' of FusionAuth, they won't be automatically logged in.)