I don't know in what context you mean. But, in constructing web pages using php, a header file is a php file that has the code for the top of the pages that you see. There may also be footer, sidebar and other php files. Those are then assembled by your host server, on the fly, for each visitor, along with the main php file for the page which makes the whole page different from other pages.
Each page of the site at
is basically constructed of a common header file, sidebar file, and footer file, along with a separate main file for each page. So if you look at different pages on that site, you will see that the top, bottom, and side of each page looks the same, but the main parts are different.