PDFEncrypt

PDFEncrypt is a free, open-source PDF encryption utility, making it easy to encrypt any PDF. With PDFEncrypt, you don't need to purchase expensive software or spend time searching for the right options. Just select the PDF you want to encrypt and enter a password, and your file is encrypted with industry-standard algorithms compatible with Adobe Reader.

PDFEncrypt is completely free and open-source (AGPL) and offers additional features such as the ability to select PDF file permissions (allow printing, form filling, etc) and launch other applications after successful encryption. PDFEncrypt can be used as a stand-alone utility or in a toolset of other utilities designed to process PDF files.