To give you an example what should only be in header.php
if you want to include your menu/navigation on all your pages.
<nav role="navigation">
<a href="home.php"><img src="img/logo.svg" alt="logo" /></a>
<ul>
<li><a href="home.php">home</a></li>
<li><a href="portfolio.php">portfolio</a></li>
<li><a href="services.php">services</a></li>
<li><a href="contact.php">contact</a></li>
</ul>
</nav>
You see? no html, no head and no body tags... just the mark-up for your menu.
This can then be included into your header for example like this:
<!doctype html>
<html>
<head>
<!-- All your meta data & stylesheets in here -->
</head>
<body>
<header>
<?php include 'header.php';?>
</header>
<main role="main">
<!-- main content -->
</main>
<footer>
<!-- footer content -->
</footer>
</body>
</html>