Most store owners have preferences when it comes to using certain payment gateways. You might prefer most of your revenue going through a payment gateway that accepts credit cards, like Stripe, but still allow users to use PayPal. For situations like this, you can charge an extra fee on the order based on the payment gateway, to encourage users to use the cheaper option.
You should install and activate the Payment Gateway based Fees extension available on WooThemes.com.
In order to add a fee per gateway using Payment Gateway based Fees, go through the following steps:
From the WordPress admin, go to WooCommerce | Settings | Additional Fees.
Click on the payment gateway that you'll be adding a fee to:
Check the Enable additional fees on total cart value for this gateway setting.
Select how you'd like to charge the additional fee in the Type of additional fee dropdown.