FileZilla does not have any command line arguments (nor any other way) that allow an automatic transfer.
Some references:
Though you can use any other client that allows automation.
You have not specified, what protocol you are using. FTP or SFTP? You will definitely be able to use WinSCP, as it supports all protocols that FileZilla does (and more).
Combine WinSCP scripting capabilities with Windows Scheduler:
A typical WinSCP script for upload (with SFTP) looks like:
open sftp://user:[email protected]/ -hostkey="ssh-rsa 2048 xxxxxxxxxxx...="
put c:\mypdfs\*.pdf /home/user/
close
With FTP, just replace the sftp:// with the ftp:// and remove the -hostkey="..." switch.
Similarly for download: How to schedule an automatic FTP download on Windows?
WinSCP can even generate a script from an imported FileZilla session.
For details, see the guide to FileZilla automation.
(I'm the author of WinSCP)
Another option, if you are using SFTP, is the psftp.exe client from PuTTY suite.