There are several ad plugins that allow you to do things like this. Have you looked into them? This is one I like to use: http://wordpress.org/plugins/adrotate/, but there are several others that also allow ads to be placed within posts.
Otherwise you will have to modify the php code for your homepage.
I just changed index.php and added some code. Here it is if anyone cares.
<?php if ( have_posts() ) : ?>
<?php $count = 1; ?>
<?php while ( have_posts() ) : the_post(); ?>
<?php get_template_part( 'content', ( post_type_supports( get_post_type(), 'post-formats' ) ? get_post_format() : get_post_type() ) ); ?>
<?php if ( is_singular() ) comments_template(); // Loads the comments.php template. ?>
<?php if($count == 1):?>
<div class="ad-homepage">
// Ad code goes here
</div>
<?php endif;?>
<?php $count++;?>
<?php endwhile; ?>
<?php else : ?>
<?php get_template_part( 'loop-error' ); // Loads the loop-error.php template. ?>
<?php endif; ?>
