qpdf: Encrypt a PDF with Linux
If you are running on Windows, you can use Windows Subsystem for Linux (WSL) to achieve the same result.
qpdf --encrypt '$uPer.53cre7!' '$uPer.53cre7!' 256 -- \
/mnt/c/Users/user.name/Desktop/document.pdf \
/mnt/c/Users/user.name/Desktop/document.protected.pdf
Example using qpdf from WSL to encrypt a PDF with AES-256