Systems and methods are described for using a mobile phone to remotely control a computing device. In one implementation, a communication channel between the mobile phone and the computing device uses an overlay network, such as an instant messaging (IM) service, to exchange communication data packets. An exemplary system includes a flexible layered architecture—which allows tailoring the system for remote control of various applications using various network configurations. Based on the overlay protocol used, a transport protocol layer can provide helpful application programming interfaces (APIs). On top of the transport protocol layer, a remote control protocol defines a framework for packet exchange of extensible commands, customizable for remote control of diverse applications. Use of paired-key encryption, IM accounts, and buddy lists ensure that communications between mobile phone and remote computer are secure.