How to timeout a thread

Indeed rather use ExecutorService instead of Timer, here’s an SSCCE:

package com.stackoverflow.q2275443;

import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.TimeoutException;

public class Test {
    public static void main(String[] args) throws Exception {
        ExecutorService executor = Executors.newSingleThreadExecutor();
        Future<String> future = executor.submit(new Task());

        try {
            System.out.println("Started..");
            System.out.println(future.get(3, TimeUnit.SECONDS));
            System.out.println("Finished!");
        } catch (TimeoutException e) {
            future.cancel(true);
            System.out.println("Terminated!");
        }

        executor.shutdownNow();
    }
}

class Task implements Callable<String> {
    @Override
    public String call() throws Exception {
        Thread.sleep(4000); // Just to demo a long running task of 4 seconds.
        return "Ready!";
    }
}

Play a bit with the timeout argument in Future#get() method, e.g. increase it to 5 and you’ll see that the thread finishes. You can intercept the timeout in the catch (TimeoutException e) block.

Update: to clarify a conceptual misunderstanding, the sleep() is not required. It is just used for SSCCE/demonstration purposes. Just do your long running task right there in place of sleep(). Inside your long running task, you should be checking if the thread is not interrupted as follows:

while (!Thread.interrupted()) {
    // Do your long running task here.
}