The present disclosure relates to a method and a device for encrypting an application, belonging to a field of computer technology. The method includes: receiving a foreground running request sent by the application, in which the foreground running request includes a system account ID of a system account logged in a system currently; detecting whether the system account ID is a main account ID of the system; replacing the system account ID with the main account ID of the system if the system account ID is not the main account ID of the system; and determining an encryption algorithm for the application in the system the main account logged in, and encrypting the application according to the encryption algorithm.