In addition to its package-oriented focus, RPM is designed to support upgrading packages. Once an application has been installed from an RPM package, a newer version of the same application can be installed using RPM. Doing so upgrades the existing application, removing its old files and replacing them with new files. In addition, however, RPM takes care to preserve any customizations that have been made to that application. The Apache Web server application, for example, is commonly installed on Linux machines that need the ability to serve Web pages.

Apache's configuration information, which specifies things such as which files on the system should be made available as Web pages and who should be able to access those Web pages, is stored in a text file, typically /etc/httpd/conf/httpd.conf. Suppose Apache has been installed using RPM and that you have then customized httpd.conf to specify its configuration. If you upgrade Apache using RPM, as part of the upgrade procedure, the RPM application will take precautions to preserve the customizations you have made to the Apache configuration. In contrast, manual upgrades of applications often overwrite any existing configuration files, losing all site customizations the system administrator has made.