First, write your script and save the .js file in your theme, preferably in a folder within your theme for organization (e.g. /your-theme/js/your-script.js)

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jQuery(function($) {

  $('#nav a').last().addClass('last');

})

Next, open functions.php within your theme

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add_action( 'wp_enqueue_scripts', 'add_my_script' );

function add_my_script() {

    wp_enqueue_script(

        'your-script', // name your script so that you can attach other scripts and de-register, etc.

        get_stylesheet_directory_uri() . '/js/your-script.js', // this is the location of your script file

        array('jquery') // this array lists the scripts upon which your script depends

    );

}

Here’s the script without comments:

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add_action( 'wp_enqueue_scripts', 'add_my_script' );

function add_my_script() {

    wp_enqueue_script('your-script', get_stylesheet_directory_uri() . '/js/your-script.js', array('jquery'));

}