Not if the resulting HTML is what you would want anyway for SEO purposes. However, you might want to make sure that whatever you use for the "header" includes a way to get any page-specific info into it (such as meta tags keywords/descriptions). I often write them as PHP functions that accept parameters, so the calling page can require_once() the function definitions, then invoke the functions to get the customized output, e.g.:
<?php require_once $_SERVER['DOCUMENT_ROOT'].'/includes/html_funcs.php'; echo htmlHeader('keyword1, keyword2, keyword3', 'This is a description'); ?>
"Please give us a simple answer, so that we don't have to think, because if we think, we might find answers that don't fit the way we want the world to be."
~ Terry Pratchett in Nation
Since the server side php code is not seen on the front end (by the search crawlers), it won't have an impact as long as your resulting html is seo friendly. In fact there's no real way (besides the file extension) for the crawler to even know the site is coded in php.