We aim to find and characterize the Lyman-alpha Emitting objects (LAEs) in the J-PAS survey. LAEs are objects which present a Lyman-alpha (Lyα) emission line (1216 Å) with a rest-frame equivalent width of EW0 < 20 Å. The strong Lyα emission is produced by recombination of hydrogen atoms ionized by young stars at regions of high star formation or by the activity of an Active Galactic Nucleus (AGN). Identifying Lyα-emitting sources and building their luminosity census is a fundamental step in order to understand a multitude of processes in the high-z Universe ranging from small to large scales, such as: star formation in young galaxies, the role of AGN fuelling and feedback in the early phases of galaxy assembly as well as the formation of structures at high-z. We build the Lyman-alpha luminosity function for the J-PAS pathfinder surveys (miniJPAS & J-NEP), in ~1.14 deg2 in the redshift interval z=2-3.5. We also forecast the performance of J-PAS and the expected scientific output in the field of Ly-alpha emission at high-z.