cod-add-fee.php

<?php

add_action( 'woocommerce_checkout_create_order', function( $order, $data ) {
        // For my example I only want to do this on payments through cash on delivery gateway
        // This is not a requirement though, you can do it for any reason you want.
  	if ( $order->get_payment_method() !== 'cod' ) {
		return;
	}

        // I get my fee from the COD gateway settings field we added
	$cod = new \WC_Gateway_COD();
	$fee = (float) $cod->settings[ 'custom_fee' ];

	if ( $fee <= 0 ) {
		return;
	}

	$item = new \WC_Order_Item_Fee();
	$item->set_props( array(
		'name'      => __( 'Cash on delivery fee', 'textdomain' ),
		'tax_class' => 0,
		'total'     => $fee,
		'total_tax' => 0,
		'order_id'  => $order->get_id(),
	) );
	$item->save();

	$order->add_item( $item );
	$order->calculate_totals();
} );