try {
    Connection conn = db.getConnection() ;
    StringBuilder sql = new StringBuilder() ;
    sql.append("VACUUM");

    //PreparedStatement prep = conn.prepareStatement(sql.toString()) ;
    Statement stat = conn.createStatement() ;
    boolean rs = stat.execute(sql.toString()) ;

    System.out.println("Executed vacuum " + rs ) ;

    //Testing code--preparedstatement attempts
    //conn.setAutoCommit(false);
    //boolean rs = prep.execute() ;
    //conn.setAutoCommit(true);

    } catch (Exception e) {
       //Edited back in after posting to StackOverflow
        System.out.println(
                ".SQLiteVacuum :: exception " +
                e.getMessage() + " " + e.getClass().getName() );
        e.printStackTrace() ;
    }

private final String dbJDBCdriverclassname = "org.sqlite.JDBC" ;
private final String dbJDBCpreconnectionstring = "jdbc:sqlite:" ;
        // Setup the driver reference
        Class.forName(dbJDBCdriverclassname) ; //"org.sqlite.JDBC"

        // Create the connection string
        String connstring = dbJDBCpreconnectionstring + this.getDBConnectionFullFileName() ;

        // create the connection
        dbconnection =
                DriverManager.getConnection(connstring) ; // "jdbc:sqlite:test.db"

Statement stmt = null;
ResultSet rs = null;
try {
    Connection conn = DBConnection.getConnection();//something to get a connection
    stmt = conn.createStatement();
    stmt.executeUpdate("VACUUM");
} catch (SQLException ex) {
    //Something if you like, or not you're the boss!
} finally {
    DBConnection.closeResources(rs, stmt);//something to close all the resources
}