A software upgrade tool and procedure provide uninterrupted operation of a replication system during an upgrade of software components of the system. The replication system includes one or more user systems coupled to one or more target storage systems over a communications network, such as a computer network. Illustratively, each user system is embodied as a replication client, while each target storage system is embodied as a replication server. In addition, the replication system includes a management system embodied as a management server that manages configuration of the system, including during upgrade of the software components of the replication system. To that end, the software upgrade tool cooperates with the management server to query the configuration of “old” versions of the software components and to manage upgrades of those components to “new” versions of software. According to the invention, the upgrade tool and procedure enable both the old and new versions of the software components to run concurrently on the replication client and replication server, as well as the management server.