I assume that by *.scp file you mean WinSCP script file (which have no specific extension).
If that's correct, use EncryptKeyPlain raw session settings:
https://winscp.net/eng/docs/rawsettings#encryptkeyplain

The easiest is to use your GUI settings to generate a script template:
https://winscp.net/eng/docs/ui_generateurl#script

Is there a WinSCP encryption line command to use it in a *.scp file? The goal is to systematically upload an encrypted file to an SFTP server. Currently I have a WinSCP session setup to encrypt files but only works using the GUI, so it's a manual drag and drop process.