scrollIntoView() is not working: does not taking in account fixed element

Your question is answered in this link.

var node = 'select your element';
var yourHeight = 'height of your fixed header';

// scroll to your element
node.scrollIntoView(true);

// now account for fixed header
var scrolledY = window.scrollY;

if(scrolledY){
  window.scroll(0, scrolledY - yourHeight);
}

Also you can use this way:

let item = // what we want to scroll to
let wrapper = // the wrapper we will scroll inside
let count = item.offsetTop - wrapper.scrollTop - xx // xx = any extra distance from top ex. 60
wrapper.scrollBy({top: count, left: 0, behavior: 'smooth'})

Source: https://github.com/iamdustan/smoothscroll/issues/47

You can make the window scrollTo x position 0 and y position the element's offsetTop subtracted by the fixed element's offsetHeight.

JSFiddle with your code: http://jsfiddle.net/3sa2L14k/

.header{
  position: fixed;
  background-color: green;
  width: 100%;
  top: 0;
  left: 0;
  right: 0;
}
html, body{
  height: 1000px;
}

#toBeScrolledTo{
  position: relative;
  top: 500px;
}

<div class="header">
Header
</div>
<div id="toBeScrolledTo">
Text Text Text
</div>
<script>
window.scrollTo(0, document.getElementById('toBeScrolledTo').offsetTop - document.getElementsByClassName('header')[0].offsetHeight);
</script>