This catalogue contains the emission-line fluxes for galaxies in miniJPAS (Bonoli et al. 2019), J-NEP (Hernán-Caballero et al. 2023) and J-PAS EDR (Vázquez Ramió et al. in prep.), derived from the J-PAS narrow-band filter spectrophotometry after continuum subtraction using SED fitting (see Fernández-Ontiveros et al. 2026 for details). The catalogue tables are structured as follows:# The first columns contain information for each source, taken from the J-PAS catalogues. ID Source identification number, corresponding to TILE_ID-NUMBER in J-PAS z Photo-z estimate from J-PAS catalogue imag i-band AB magnitude in the J-PAS photometric catalogue, corresponding to the AUTO aperture # The rest of the columns correspond to the line (e.g. [OIII]5007A) or blend flux (e.g. Halpha + [NII]6548,6583 A), associated error, and continuum determined from the SED fitting measured for each target. For instance: o3_5007 [OIII]5007A line flux in units of 1.e-15 erg/cm2/s err_5007 [OIII]5007A line flux uncertainty in units of 1.e-15 erg/cm2/s cont_5007 [OIII]5007A continuum flux spectral density in units of 1.e-15 erg/cm2/s/AA ha+n2_6565 Halpha+[NII]6548,6583A blend flux in units of 1.e-15 erg/cm2/s err_6565 Halpha+[NII]6548,6583A blend flux uncertainty in units of 1.e-15 erg/cm2/s cont_6565 Halpha+[NII]6548,6583A blend continuum flux spectral density in units of 1.e-15 erg/cm2/s/AA ... ...