Provided are a computer program product, system, and method for performing workload balancing of tracks in storage areas assigned to processing units. For each processing unit, there is an assignment of a storage area of tracks in the storage to the processing unit, at least one queue having I/O requests to the storage area, and queue usage information indicating a quantity related to the I/O requests in the at least one queue. A determination is made from the queue usage information whether to perform workload balancing for a source processing unit having at least one source queue. A target processing unit is selected in response to determining to perform the workload balancing for the source processing unit. Tracks in a source storage area assigned to the source processing unit are moved to a target storage area assigned to the target processing unit.