в чем проблема так сделать ?
onStart()
StartTime = System.currentTimeMillis();
...
OnChronometerTickListener
...
long elapsedTimeMills = System.currentTimeMillis() - StartTime
final long sec = elapsedTimeMills / 1000;
final int hours = (int) sec / 3600;
final int min = (int) (sec % 3600) / 60;
final int seconds = (int) sec % 60;
txtTimer.setText(String.format("%02d:%02d:%02d", hours, min, seconds));