Edit in JSFiddle

/* 
  Inital version @http://jsfiddle.net/U64Xr/5/ is not accurate
  because the timer resolution of a browser isn't.
  Thus, you'll need a more granular measure like performance.now().
*/
(_ => {
  let starttime, interval;
  const d2 = `2-digit`;
  const timeOpts = { hour: d2, minute: d2,  second: d2,  fractionalSecondDigits: 3, hour12: false };
  const timer = document.querySelector('#time');
  const formatDate = (d = new Date()) => new Intl.DateTimeFormat('en', timeOpts).format(d);
  const padLeft = (number = `0`, len = 2, chr = `0`) => `${number}`.padStart(len, chr);
  const timeDiff = (milliseconds = 0) => {
  	milliseconds = Math.abs(milliseconds);
    return `${
    	padLeft(Math.floor(((milliseconds / 1000) / 60) / 60) % 24)}:${
      padLeft(Math.floor((milliseconds / 1000) / 60) % 60)}:${
      padLeft(Math.floor(milliseconds / 1000) % 60)}.${
      padLeft(Math.floor(milliseconds % 1000), 3)}`;
  };
  const updateTimer = (diff = 0) => timer.textContent = diff < 1 ? `00:00:00.000` : timeDiff(diff);
  const addTT = txt => timer.setAttribute('data-tt', `${timer.getAttribute('data-tt')}\n${txt}`);
  const run = _ => updateTimer(performance.now() - starttime);
  const stop = _ => {
      clearInterval(interval || 0);
      addTT(starttime ? `Stopped: ${formatDate()}` : ``);
	};
	const reset = _ => {
      stop();
      starttime = undefined;
      updateTimer();
	};
  const start = _ => {
      clearInterval(interval || 0);
      addTT(`${starttime ? `Resumed` : `Started`}: ${formatDate()}`);
      starttime = starttime || performance.now();
      interval = setInterval(run, 50);
  };    
  const actions = { start,  stop,  reset, };
  document.body.addEventListener( `click`, evt => 
  	evt.target.id in actions ? actions[evt.target.id]() : true );
})();

<div id="time" data-tt="Hours, Minutes, Seconds, MilliSeconds&#x0A;Note: stopwatch runs from starttime, so resuming&#x0A;(clicking start/continue after having paused) may show a gap">00:00:00.000</div>
<div id="ctrl">
    <button id="start">START/CONTINUE</button>
    <button id="stop">PAUSE</button>
    <button id="reset">RESET</button>
</div>

body {
    font: 12px normal verdana, arial;
}

#time {
    width: 300px;
    font-family: "Segoe UI",Roboto,Ubuntu,sans-serif;
    margin: 25px auto;
    border: 1px solid #000;
    padding: 10px;
    text-align: center;
    font-size: 2em;
    background: #efefef;
    box-shadow: 1px 1px 5px #888;
    border-radius: 5px;    
}

[data-tt]:before {
    content: attr(data-tt);
    opacity: 0;
    height: 1em;
    position: absolute;  
    top: -1000em;
    font-size: 0.6em;
    padding: 6px;
    max-width: 400px;
    border: 1px solid #888;
    background: white;
    white-space: pre;
    text-align: left;
    border-radius: 5px;
    box-shadow: 1px 1px 7px #888;
    transition: opacity 0.2s ease-out;
}

[data-tt]:hover:before {
    opacity: 1;
    top: auto;
    height: auto;
    margin-top: 2em;
    transition: opacity 0.4s 0.5s ease-in;
}


#ctrl {
    text-align: center;    
}