You can simply create a cron.php next to your index.php with the following content:
<?php
define('DS', DIRECTORY_SEPARATOR);
// load kirby
require(__DIR__ . DS . 'kirby' . DS . 'bootstrap.php');
$kirby = kirby();
$kirby->configure();
$kirby->cache()->flush();
This can be called in the cronjob with curl for example: http://yourdomain.com/cron.php
You might want to add some kind of token check though, so only your cronjob can really flush your cache.