The JEM-EUSO instrument is a wide-angle refractive telescope in near-ultraviolet wavelength region being proposed for attachment to the Japanese Experiment Module (JEM) onboard International Space Station (ISS). The main scientific goal of the mission is the study of Extreme Energy Cosmic Rays (EECR) above 5 × 1019 eV. The instrument consists of high transmittance optical Fresnel lenses with a diameter of 2.5 m, a focal surface covered by ∼ 5000 Multi Anode Photo Multiplier Tubes of 64 pixels, front-end readout, trigger and system electronics.The EUSO-Balloon experiment is a pathfinder mission in which a telescope of smaller dimension than the one designed for the ISS will be mounted onboard a stratospheric balloon. The main objective of this pathfinder mission, planned for 2014, is to perform a full scale end-to-end test of all the key technologies and instrumentation of JEM-EUSO detectors and to prove the global detection chain. Furthermore, EUSO-Balloon will measure the atmospheric and terrestrial UV background components, in different observational modes, fundamental for the development of the simulations. Through a series of stratospheric balloon flights performed by the French Space Agency CNES, EUSO-Balloon also has the potential to detect Extensive Air Showers from above, paving the way for any future large scale, space-based EECR observatory.In this paper we will present the Data Processor (DP) of EUSO-Balloon, which is the component of the Electronics System which performs the data management and the instrument control. More in detail, the DP controls the front-end electronics, performs the 2nd level trigger filtering, tags events with arrival time and payload position through a GPS system, manages the Mass Memory for data storage, measures live and dead time of the telescope, provides signals for time synchronization of the event, performs housekeeping monitor, and handles the interface to the telemetry system. The DP has to operate at high altitude in unpressurized environment, and this represents a technological challenge for heat dissipation. We will describe the main components of the system, the state-of-the-art and the results of the tests carried out.