Something like this should work if the images are linked to "image file". Put this in a javascript file and enqueue the file after jQuery is ready.

jQuery(document).ready(function($) {
        $(".gallery-icon a").magnificPopup();
    });

I have had this issue with the popup not working and for me it turned out to be a jQuery conflict. It turns out I needed to use a different jQuery version. Here is what worked for me.

After adding the magnific-popup.min.css I had to deregister the existing jQuery and enqueue version 3.5.1. Note the dependency is jquery. Here is a documentation reference.

wp_deregister_script( 'jquery' );
    wp_register_script( 'jquery', get_template_directory_uri() . '/js/jquery3.js');
    wp_enqueue_script( 'jquery', get_template_directory_uri() . '/js/jquery3.js');
    wp_enqueue_script( 'magnific-popup', get_template_directory_uri() . '/js/jquery.magnific-popup.min.js', array('jquery'), '', true );
    wp_enqueue_script( 'magnific-popup-init', get_template_directory_uri() . '/js/jquery.magnific-popup.init.js', array('jquery'), '', true );
    wp_enqueue_script( 'custom', get_template_directory_uri() . '/js/custom.js', array('jquery'), '', true );