Balmer emission may be a powerful diagnostic tool to test the paradigm of cosmic ray (CR) acceleration in young supernova remnant (SNR) shocks. The width of the broad Balmer line is a direct indicator of the downstream plasma temperature. In case of efficient particle acceleration an appreciable fraction of the total kinetic energy of the plasma is channeled into CRs, therefore the downstream temperature decreases and so does the broad Balmer line width. This width also depends on the level of thermal equilibration between ions and neutral hydrogen atoms in the downstream. Since in general in young SNR shocks only a few charge exchange (CE) reactions occur before ionization, equilibration between ions and neutrals is not reached, and a kinetic description of the neutrals is required in order to properly compute Balmer emission. We provide a method for the calculation of Balmer emission using a self-consistent description of the shock structure in the presence of neutrals and CRs. We use a recently developed semi-analytical approach, where neutral particles, ionized plasma, accelerated particles and magnetic fields are all coupled together through the mass, momentum and energy flux conservation equations. The distribution of neutrals is obtained from the full Boltzmann equation in velocity space, coupled to Maxwellian ions through ionization and CE processes. The computation is also improved with respect to previous work thanks to a better approximation for the atomic interaction rates. We find that for shock speeds >2500km/s the distribution of broad neutrals never approaches a Maxwellian and its moments differ from those of the ionized component. These differences reflect into a smaller FWHM than predicted in previous calculations, where thermalization was assumed. The method presented here provides a realistic estimate of particle acceleration efficiency in Balmer dominated shocks.