We have studied the terahertz emission from a 720 × 60 × 1.2 μm3 mesa patterned from under-doped Bi2Sr2CaCu2O8+δ. This device has an S-shaped current–voltage characteristic due to self-heating, allowing us to compare its THz emission behaviours at up to three different bias currents for the same voltage. The THz frequency generated along the lowest current branch follows the expected Josephson relation for a stack of intrinsic Josephson junctions connected in series. However, in the high current regimes, THz emission occurs at a significantly lower frequency than expected. We show that this behaviour is consistent with strongly non-uniform self-heating of the mesa at high bias currents.