The proper way to do it is using fullPage events. In this case: afterLoad
or onLeave
Take a look at the documentation for more information about how to use them.
You can take a look at this living example in which the top menu fades In or out depending on whether the user is in the first section or not: http://jsfiddle.net/J8hqM/8/
It should look like:
// Script FullPage
$.fn.fullpage({
/* whatever config you have...*/
afterLoad: function(anchor, index){
if(index == 1){
$('#menu').fadeOut();
}else{
$('#menu').fadeIn();
}
}
});