Provided are a computer program product, system, and method for pre-allocating storage space for an application operation in a space efficient volume. To transmit application requests to a storage controller managing a space efficient volume, a determination is made of an amount of space required for an application operation requiring a series of write operations over a period of time to the space efficient volume. A space pre-allocation request for the application operation is transmitted to the storage controller. The space pre-allocation request indicates a requested amount of physical space to pre-allocate to the application operation to cause the storage controller to pre-allocate the requested amount of space in advance of the application operation needing the requested amount of space in the volume for the series of write operations.