Theoretically, you'd want <h1> shown by default, in case the end user doesn't have Javascript installed, but hidden by Javascript which is called between your <head></head> tags, so that it's hidden before the page loads. Put the rest of the Javascript right before your </body> tag, so it loads lastly.
index.html
<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">
    <title>title</title>
    <script src="doFirst.js"></script>
  </head>
  <body>
    <h1 class='title'>My Title</h1>
    <!-- page content -->
    <script src="doLast.js"></script>
  </body>
</html>
doFirst.js
$(document).ready(function(){
  $("h1.title").hide();
});
Use the hide() function to hide the element.
doLast.js
$(document).ready(function(){
  $("h1.title").fadeIn(3000);
});
Use the fadeIn() function to control the fade. The number represents the fade speed in milliseconds.
See a live example on JSFiddle.
Update
You can also do this with CSS3.
See how to fade in CSS.
See how to grow font in CSS.