IBM WebSphere Application Server is the foundation of the IBM WebSphere software platform, and has included Jython as an administrative scripting language for several releases. As of the latest release (7.0) it is the preferred and recommended administrative scripting language.

A beta release of version 8.0 was made available on developerWorks on July 1, 2010.

The version of Jython included in WebSphere 6.0, 6.1, 7.0, and 8.0 is Jython 2.1, meaning that Jython users can not only write scripts to use in administrative tasks such as server startup and shutdown, application installation and updates, etc., but also write stand-alone applications using the Python HTTP servers, or using PyServlet develop and deploy Servlet-based applications.

"WebSphere Application Server Administration Using Jython" was published by IBM Press Books in October of 2009.