Provided are a computer program product, system, and method for performing a failover between a first storage system and a second storage system. Data is synchronized between the first storage system and the second storage system. A failover is performed from the first storage system to the second storage system in response to a failover event at the first storage system while synchronizing the data. A determination is made that a first storage unit of the first storage system is inoperable and that that a second storage unit of the first storage system is operable in response to the failover event. In response to determining that the second storage unit is operable, a resynchronization is initiated to copy updates to a second storage unit of the second storage system mirroring the second storage unit of the first storage system to the second storage unit of the first storage system.