Time-varying connectivity methods are increasingly used to study directed interactions between brain regions from electrophysiological signals. These methods often show good results in simulated data but it is unclear to what extent connectivity results obtained from real data are physiologically plausible. Here we introduce a benchmark approach using multichannel somatosensory evoked potentials (SEPs) measured across rat cortex, where the structural and functional connectivity is relatively simple and well-understood. Rat SEPs to whisker stimulation are exclusively initiated by contralateral primary sensory cortex (S1), at known latencies, and with activity spread from S1 to specific cortical regions. This allows for a comparison of time-varying connectivity measures according to fixed criteria. We thus evaluated the performance of time-varying Partial Directed Coherence (PDC) and the Directed Transfer Function (DTF), comparing row- and column-wise normalization and the effect of weighting by the power spectral density (PSD). The benchmark approach revealed clear differences between methods in terms of physiological plausibility, effect size and temporal resolution. The results provide a validation of time-varying directed connectivity methods in an animal model and suggest a driving role for ipsilateral S1 in the later part of the SEP. The benchmark SEP dataset is made freely available.