You need to call scrollTop() on the element with the overflow, which is the <div> element, not the <ul> element. Further you need to grab the top by element.position().top and you need to ensure that the <div> element is positioned relatively using position: relative, since the top is relative to the firstnext relative parent element.
Here's an SSCCE:
<!doctype html>
<html lang="en">
<head>
<title>SO question 2621792</title>
<script src="http://code.jquery.com/jquery-latest.min.js"></script>
<script>
$(document).ready(function() {
$('#div').scrollTop($('#li3').position().top);
});
</script>
<style>
#div {
position: relative;
overflow: auto;
width: 100px;
height: 50px;
}
</style>
</head>
<body>
<div id="div">
<ul>
<li>Item 1</li>
<li>Item 2</li>
<li id="li3">Item 3</li>
<li>Item 4</li>
<li>Item 5</li>
</ul>
</div>
</body>
</html>