Approximately 20 weeks of beamtime are provided for scientific experiments per year which are not possible on any other radiation source. It is operated in the "self-amplified spontaneous emission" (SASE) mode. Six beamlines are operational.

In the past years, an additional FEL undulator line in a separate tunnel - FLASH2- and the new 'Kai Siegbahn' experimental hall have been built adjacent to the existing FLASH facility now called FLASH1. First lasing of FLASH2 was achieved in August 2014 in parallel to FLASH1. Now, the FLASH facility at DESY comprises two separate and almost independent FEL sources. This upgrade enhances significantly the capacities for VUV and soft X-ray FEL users at DESY. Up to 6 beamlines (called FL beamlines) will be set up in the 'Kai Siegbahn' hall, FL24 and FL26 have started operation in spring 2016.

FL24 has an open port for user supplied endstations. FL24 covers the entire wavelength range of FLASH2. It offers a KB bending mirror system and a split-and-delay unit for XUV-XUV pump-probe experiments.

FL26 features the permanent end station REMI - a reaction microscope from R. Moshammer's group at MPIK Heidelberg.