How Do I Programmatically Force Custom Permalinks with My Theme?

To fully enable permalinks, you also need to ensure that .htaccess is also created. To do that, you need to set an option and flush the rules with a Boolean.

global $wp_rewrite; 

//Write the rule
$wp_rewrite->set_permalink_structure('/%postname%/'); 

//Set the option
update_option( "rewrite_rules", FALSE ); 

//Flush the rules and tell it to write htaccess
$wp_rewrite->flush_rules( true );

If you use this in a plugin, it needs to be in the init hook, not the load hook. If it’s in the load hook, it will throw an error saying $wp_rewrite is null.

Important: You should also have a conditional so this is only set once. (You can create an option and check if it’s set, if not then you run this permalink code and set that option)

I also typically check if it’s the admin side and only run it if it is.