itext Protecting your PDF

 /*
  * This class is part of the book "iText in Action - 2nd Edition"
  * written by Bruno Lowagie (ISBN: 9781935182610)
  * For more info, go to: http://itextpdf.com/examples/
  * This example only works with the AGPL version of iText.
  */

 package part3.chapter12;

 import java.io.FileOutputStream;
 import java.io.IOException;

 import com.itextpdf.text.Document;
 import com.itextpdf.text.DocumentException;
 import com.itextpdf.text.Paragraph;
 import com.itextpdf.text.pdf.PdfWriter;
 import com.itextpdf.text.pdf.PdfReader;
 import com.itextpdf.text.pdf.PdfStamper;

 public class EncryptionPdf {
     /** User password. */
     public static byte[] USER = "Hello".getBytes();
     /** Owner password. */
     public static byte[] OWNER = "World".getBytes();

     /** The resulting PDF file. */
     public static final String RESULT1
         = "results/part3/chapter12/encryption.pdf";
     /** The resulting PDF file. */
     public static final String RESULT2
         = "results/part3/chapter12/encryption_decrypted.pdf";
     /** The resulting PDF file. */
     public static final String RESULT3
         = "results/part3/chapter12/encryption_encrypted.pdf";

     /**
      * Creates a PDF document.
      * @param filename the path to the new PDF document
      * @throws DocumentException
      * @throws IOException
      */
     public void createPdf(String filename) throws IOException, DocumentException {
         // step 1
         Document document = new Document();
         // step 2
         PdfWriter writer = PdfWriter.getInstance(document, new FileOutputStream(filename));
         writer.setEncryption(USER, OWNER, PdfWriter.ALLOW_PRINTING, PdfWriter.STANDARD_ENCRYPTION_128);
         writer.createXmpMetadata();
         // step 3
         document.open();
         // step 4
         document.add(new Paragraph("Hello World"));
         // step 5
         document.close();
     }

     /**
      * Manipulates a PDF file src with the file dest as result
      * @param src the original PDF
      * @param dest the resulting PDF
      * @throws IOException
      * @throws DocumentException
      */
     public void decryptPdf(String src, String dest) throws IOException, DocumentException {
         PdfReader reader = new PdfReader(src, OWNER);
         PdfStamper stamper = new PdfStamper(reader, new FileOutputStream(dest));
         stamper.close();
         reader.close();
     }

     /**
      * Manipulates a PDF file src with the file dest as result
      * @param src the original PDF
      * @param dest the resulting PDF
      * @throws IOException
      * @throws DocumentException
      */
     public void encryptPdf(String src, String dest) throws IOException, DocumentException {
         PdfReader reader = new PdfReader(src);
         PdfStamper stamper = new PdfStamper(reader, new FileOutputStream(dest));
         stamper.setEncryption(USER, OWNER,
             PdfWriter.ALLOW_PRINTING, PdfWriter.ENCRYPTION_AES_128 | PdfWriter.DO_NOT_ENCRYPT_METADATA);
         stamper.close();
         reader.close();
     }

     /**
      * Main method.
      *
      * @param    args    no arguments needed
      * @throws DocumentException
      * @throws IOException
      */
     public static void main(String[] args) throws IOException, DocumentException {
         EncryptionPdf metadata = new EncryptionPdf();
         metadata.createPdf(RESULT1);
         metadata.decryptPdf(RESULT1, RESULT2);
         metadata.encryptPdf(RESULT2, RESULT3);
     }
 }

http://itextpdf.com/examples/iia.php?id=219