A little warning, unexpected fees at checkout can put some users off and some payment gateways do not allow custom additional fees. Passing on fees and surcharges may not be legal in your location so do check before implementing this code snippet. Adding a fixed amount fee at checkout for handling or administration costs is really easy and appears in the order summary box as an order item. Once the order is paid for, the admin fee is shown on the order received thank you page, order editor as a line item, and in all of the post-purchase emails where the order table appears.
/*
* Snippet Name: WooCommerce Add Checkout Admin/Handling Fee
* Snippet Author: ecommercehints.com
*/
add_action( 'woocommerce_cart_calculate_fees', 'ecommercehints_fixed_checkout_admin_fee', 25 );
function ecommercehints_fixed_checkout_admin_fee() {
WC()->cart->add_fee( 'Admin Fee', 5 ); // 5 being the fee value
}