How do I assert my exception message with JUnit Test annotation?

You could use the @Rule annotation with ExpectedException, like this:

@Rule
public ExpectedException expectedEx = ExpectedException.none();

@Test
public void shouldThrowRuntimeExceptionWhenEmployeeIDisNull() throws Exception {
    expectedEx.expect(RuntimeException.class);
    expectedEx.expectMessage("Employee ID is null");

    // do something that should throw the exception...
    System.out.println("=======Starting Exception process=======");
    throw new NullPointerException("Employee ID is null");
}

Note that the example in the ExpectedException docs is (currently) wrong - there's no public constructor, so you have to use ExpectedException.none().

In JUnit 4.13 you can do:

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThrows;

...

@Test
void exceptionTesting() {
  IllegalArgumentException exception = assertThrows(
    IllegalArgumentException.class, 
    () -> { throw new IllegalArgumentException("a message"); }
  );

  assertEquals("a message", exception.getMessage());
}

This also works in JUnit 5 but with different imports:

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertThrows;

...

I like the @Rule answer. However, if for some reason you don't want to use rules. There is a third option.

@Test (expected = RuntimeException.class)
public void myTestMethod()
{
   try
   {
      //Run exception throwing operation here
   }
   catch(RuntimeException re)
   {
      String message = "Employee ID is null";
      assertEquals(message, re.getMessage());
      throw re;
    }
    fail("Employee Id Null exception did not throw!");
  }