A mobile checkout system and method for completing a purchase transaction to purchase items from an internet merchant. A user browses and selects items for purchase from the merchant through a shopping application or browser (mobile or PC). During the processing of the transaction, a checkout application installed on a mobile communication device is launched. The checkout application receives a checkout token created by a checkout server that identifies the purchase transaction. After user authentication, the system uses this token and communicates with the checkout server to cause the checkout server to complete the purchase transaction, in which payment data is securely transmitted and wherein a one-time-use cryptogram can be part of the payment information.