We can directly put it in the header section as we normal does but sometime it maynot work in case of admin.
We can include following code in function.php
function mytheme_custom_scripts() { if ( ! is_admin() ) { $scriptsrc = get_stylesheet_directory_uri() . '/js/'; wp_register_script( 'myhandle', $scriptsrc . 'myscript.js', 'jquery', false ); wp_enqueue_script( 'myhandle' ); } } add_action( 'wp_enqueue_scripts', 'mytheme_custom_scripts' );
and for case of css add the following code
wp_enqueue_style('thickbox', get_bloginfo('siteurl') . 'wp-includes/js/thickbox/thickbox.css', false, false, 'screen'); wp_enqueue_script('mthickbox');
Source:http://wordpress.org/support/topic/how-can-i-add-custom-javascript-and-stylesheet-in-headerphp-file-1