A method and system for executing scripts on virtual machines is provided. The system includes an executor service that accepts scripts, parameters, authentication information from another process that needs to invoke a script on a target virtual machine (or group of virtual machines). The executor service remains running even after a script has completed execution. The executor service accepts any number of scripts and places them in a command queue. Agents running on the target virtual machine(s) check-in with the executor service to receive scripts from the command queue. Also, the executor service may directly invoke a script using a persistent connection to a virtual machine management center.