How to add woocommerce cash on delivery extra fee without plugin

Note: All payment methods are only available on Checkout page.

The following code will add conditionally a specific fee based on the chosen payment method:

// Add a custom fee (fixed or based cart subtotal percentage) by payment
add_action( 'woocommerce_cart_calculate_fees', 'custom_handling_fee' );
function custom_handling_fee ( $cart ) {
    if ( is_admin() && ! defined( 'DOING_AJAX' ) )
        return;

    $chosen_payment_id = WC()->session->get('chosen_payment_method');

    if ( empty( $chosen_payment_id ) )
        return;

    $subtotal = $cart->subtotal;

    // SETTINGS: Here set in the array the (payment Id) / (fee cost) pairs
    $targeted_payment_ids = array(
        'cod' => 8, // Fixed fee
        'paypal' => 5 * $subtotal / 100, // Percentage fee
    );

    // Loop through defined payment Ids array
    foreach ( $targeted_payment_ids as $payment_id => $fee_cost ) {
        if ( $chosen_payment_id === $payment_id ) {
            $cart->add_fee( __('Handling fee', 'woocommerce'), $fee_cost, true );
        }
    }
}

You will need the following to refresh checkout on payment method change, to get it work:

// jQuery - Update checkout on payment method change
add_action( 'woocommerce_checkout_init', 'payment_methods_refresh_checkout' );
function payment_methods_refresh_checkout() {
    wc_enqueue_js( "jQuery( function($){
        $('form.checkout').on('change', 'input[name=payment_method]', function(){
            $(document.body).trigger('update_checkout');
        });
    });");
}

Code goes in functions.php file of your active child theme (or active theme). tested and works.