The cubic-kilometre neutrino telescope, which consists of large-scale 3D-arrays of photomultiplier tubes (PMTs) currently under construction on the Mediterranean seabed, relies on accurate calibration procedures in order to answer its science goals. These proceedings present the gain calibration method used in KM3NeT, which is based on highly compressed PMT hit information. In particular, it is shown that the PMT gains can be tuned to within 2% of the nominal value, based on the measured single photoelectron time-over-threshold distribution of each PMT.