This work presents X-Shooter/Very Large Telescope spectra of the prototypical, isolated Herbig Ae stars HD 31648 (MWC 480) and HD 163296 over five epochs separated by timescales ranging from days to months. Each spectrum spans over a wide wavelength range covering from 310 to 2475 nm. We have monitored the continuum excess in the Balmer region of the spectra and the luminosity of 12 ultraviolet, optical, and near-infrared spectral lines that are commonly used as accretion tracers for T Tauri stars. The observed strengths of the Balmer excesses have been reproduced from a magnetospheric accretion shock model, providing a mean mass accretion rate of 1.11 × 10−7 and 4.50 × 10−7M yr−1 for HD 31648 and HD 163296, respectively. Accretion rate variations are observed, being more pronounced for HD 31648 (up to 0.5 dex). However, from the comparison with previous results it is found that the accretion rate of HD 163296 has increased by more than 1 dex, on a timescale of ∼15 yr. Averaged accretion luminosities derived from the Balmer excess are consistent with the ones inferred from the empirical calibrations with the emission line luminosities, indicating that those can be extrapolated to HAe stars. In spite of that, the accretion rate variations do not generally coincide with those estimated from the line luminosities, suggesting that the empirical calibrations are not useful to accurately quantify accretion rate variability.