In this paper we aim to validate a methodology designed to obtain Hα emission line fluxes from J-PLUS photometric data. J-PLUS is a multi narrow-band filter survey carried out with the 2 deg² field of view T80Cam camera, mounted on the JAST/T80 telescope in the OAJ, Teruel, Spain. The information of the twelve J-PLUS bands, including the J0660 narrow-band filter located at rest-frame Hα, is used over the first 42 deg² observed to retrieve de-reddened and [NII] decontaminated Hα emission line fluxes of 46 star-forming regions with previous SDSS and/or CALIFA spectroscopic information. The agreement between the J-PLUS Hα fluxes and those obtained with spectroscopic data is remarkable, finding a median comparison ratio with a scatter of $ \mathcal{R}\,{=}\,F^{\mathrm{J-PLUS}}_{\mathrm{H\alpha}}/F^{\mathrm{spec}}_{\mathrm{H\alpha}}\,{=}\,1.05\,{±}\,0.25 $. This demonstrates that it is possible to retrieve reliable Hα emission line fluxes from J-PLUS photometric data. With an expected area of thousands of square degrees upon completion, the J-PLUS dataset will allow the study of several star formation science cases in the nearby universe, as the spatially resolved star formation rate of nearby galaxies at z ≤ 0.015, and how it is influenced by the environment, morphology, stellar mass, and nuclear activity. As an illustrative example, the close pair of interacting galaxies NGC 3994 and NGC 3995 is analysed, finding an enhancement of the star formation rate not only in the centre, but also in outer parts of the disk of NGC 3994.