Abstract The 1215.67 Å H i Lyα emission line dominates the ultraviolet flux of low-mass stars, including the majority of known exoplanet hosts. Unfortunately, strong attenuation by the interstellar medium (ISM) obscures the line core in most stars, requiring the intrinsic Lyα flux to be reconstructed based on fits to the line wings. We present a test of the widely used Lyα emission-line reconstruction code lyapy using phase-resolved, medium-resolution STIS G140M observations of the close white dwarf–M dwarf binary EG UMa. The Doppler shifts induced by the binary orbital motion move the Lyα emission line in and out of the region of strong ISM attenuation. Reconstructions of each spectrum should produce the same Lyα profile regardless of phase, under the well-justified assumption that there is no intrinsic line variability between observations. Instead, we find that the reconstructions underestimate the Lyα flux by almost a factor of 2 for the lowest velocity, most attenuated spectrum, due to a degeneracy between the intrinsic Lyα and ISM profiles. Our results imply that many stellar Lyα fluxes derived from G140M spectra reported in the literature may be underestimated, with potential consequences for, for example, estimates of extreme-ultraviolet stellar spectra and ultraviolet inputs into simulations of exoplanet atmospheres.