<div id="elementID">
</div>

#elementID {
  width: 200px;
  height: 200px;
  background-color: red;
}

var yourElement = document.getElementById("elementID");
var opcty = 1; // opacity value
function fade() {
  opcty = opcty - 0.05; // gives 20 steps of opacity
  yourElement.style.opacity = opcty.toString();
  if (opcty > 0) setTimeout(fade, 200); // 200ms per step
  else yourElement.style.opacity = "1.0"; // show element again
}
yourElement.addEventListener("click", function () {
  setTimeout(function () {
    // fadeout logic goes here
    fade();
    // remove an element logic goes here
  }, 5000);
});