There are two kinds of fees: one that Shopify charges and another that you have to pay to the payment gateway processor you use (e.g. PayPal or credit card payment processors such as Stripe or Authorize.net).
Depending on your pricing tier, Shopify would charge somewhere between 0,5% and 2% plus the payment processor’s fee (typically 3% + 30¢). You can avoid Shopify’s fees by using the Shopify Payments gateway (only available in USA, UK, Ireland, Canada and a few other countries).