Good practices in calling javascript scripts

Question

I have some pages that use specific javascript files/scripts and do not include in the header of the site, because not all pages would use it, I wonder if it is a good practice to include Js files/codes in different parts of the page without being in the header, and if this reduces the loading speed?

<header>

js file. -- here will be included by all pages that have the header

Another specific page:

<header>

<content>

js file. -- including the js file in a separate part of the header on a specific page...