How does JProgressbar work?

Remove the part BufferedReader

along with the loop while (line != null) {

, leave only the read loop where you read bytes and update md5 - here you must update your progressBar as well. After such changes, it may look like this:

import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.IOException;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.JButton;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JProgressBar;
import javax.swing.JTextField;
import javax.swing.SwingWorker;

public class ProgressBarTest implements ActionListener, PropertyChangeListener {
    JFrame f;
    JPanel p;
    BorderLayout bdl;
    JButton cf;
    JTextField tf1;
    JLabel ls;
    JProgressBar progressBar;
    JFileChooser fc;
    File sf;
    FileInputStream fis;
    String hexRes1;
    String hexRes2 = "";
    private Task task;
    private int progress;
    String selection;

    public static void main(String[] args) {
        new ProgressBarTest().startApp();// TODO code application logic here
    }

    private void startApp() {
        f = new JFrame();
        p = new JPanel();
        bdl = new BorderLayout();
        cf = new JButton("Check-File");
        ls = new JLabel();
        tf1 = new JTextField();
        progressBar = new JProgressBar(0, 100);
        progressBar.setValue(0);
        progressBar.setStringPainted(true);

        p.setLayout(bdl);
        p.add(BorderLayout.NORTH, cf);
        p.add(BorderLayout.CENTER, ls);
        p.add(BorderLayout.WEST, tf1);
        p.add(BorderLayout.SOUTH, progressBar);

        fc = new JFileChooser();
        cf.addActionListener(this);

        f.getContentPane().add(p);
        // f.pack();
        f.setTitle("ProgressTest");
        f.setSize(950, 350);
        f.setResizable(false);
        f.setVisible(true);
        f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    }

    @Override
    public void actionPerformed(ActionEvent e) throws NullPointerException {
        // System.out.println(javax.swing.SwingUtilities.isEventDispatchThread());
        // choose a file when the button cf is clicked
        if (e.getSource() == cf) {
            int returnVal = fc.showOpenDialog(p);
            fc.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
            if (returnVal == JFileChooser.APPROVE_OPTION)
                sf = fc.getSelectedFile();
            // empty the values
            tf1.setText("");
            hexRes2 = "";
            // start the task to calculate the file
            task = new Task();
            task.addPropertyChangeListener(this);
            task.execute();
            ls.setText("Wait !");
        }
    }

    class Task extends SwingWorker<Void, Void> {
        /*
         * Main task. Executed in background thread.
         */
        @Override
        public Void doInBackground() throws InterruptedException, IOException {
            // progressbar variables to go thru the file
            setProgress(0);
            int progress = 0;
            // BufferedReader br = new BufferedReader(new FileReader(sf));
            // String line = br.readLine();
            long readLength = 0;
            long totalLength = sf.length();
            double lengthPerPercent = 100.0 / totalLength;
            // Thread.sleep(1000);
            // while the line of the file isn't empty execute
            try {
                // while (line != null) {
                // Thread.sleep(100);
                fis = new FileInputStream(sf);
                // digest calculation
                MessageDigest md = MessageDigest.getInstance("MD5");

                byte[] b = new byte[1024];
                int readed;
                while ((readed = fis.read(b)) >= 0) {
                    md.update(b, 0, readed);
                    // calculate progress.;
                    readLength = readLength + readed;
                    progress = (int) (lengthPerPercent * readLength);
                    setProgress(progress);
                }
                setProgress(100);
                fis.close();
                byte[] ba = md.digest();

                for (int j = 0; j < ba.length; j++) {
                    hexRes1 = Integer.toHexString((ba[j] & 255) | 256).substring(1);
                    hexRes2 += hexRes1;
                }

                // line = br.readLine();
                // } //printing the value
                tf1.setText(hexRes2);

            } catch (IOException | NoSuchAlgorithmException ex) {
                Logger.getLogger(ProgressBarTest.class.getName()).log(Level.SEVERE, null, ex);
            } catch (NullPointerException ex) {
                f.repaint();
            } finally {
                fis.close();
            }
            return null;
            // System.out.println(javax.swing.SwingUtilities.isEventDispatchThread());
        }
        /*
         * Executed in event dispatching thread
         */
        public void done() {
            progressBar.setValue(0);
            ls.setText("Done!\n");
        }
    }


    /**
     * Invoked when task progress property changes.
     */
    public void propertyChange(PropertyChangeEvent evt) {
        if (evt.getPropertyName().equals("progress")) {
            int progress = (Integer) evt.getNewValue();
            progressBar.setValue(progress);
        }
    }
}