First and second controllers implemented on computing equipment may be used to control switches in a network. The switches may forward network packets between end hosts. The second controller may identify first and second redundant partitions of switches in the network that are each coupled to all of the end hosts. The first controller may instruct the first partition to install software while the second partition forwards network traffic and may instruct the second partition to install software while the first partition forwards network traffic. The first controller may install the software while the second controller is active and the second controller may install the software while the first controller is active. In this way, the switches and controllers may be provided with an uninterrupted software upgrade and packets may be forwarded between end hosts during the software upgrade without introducing packet loss or other noticeable reductions in network performance.