We present THe and ZHe data for basement samples across the Kaapvaal craton to investigate the cratonic burial and erosion history during the assembly and breakup of the Rodinia supercontinent. THe and ZHe dates vary from 1187 to 135 Ma and 997 to 32 Ma, respectively. Both are negatively correlated with effective U concentration, consistent with lower He retentivity at higher radiation damage dose. The oldest THe dates, combined with volcanic rocks that document the basement was at the surface at ∼1.4 Ga, require heating to ≥130°C at ∼1.0-1.2 Ga to cause complete He loss from the titanites. We attribute this Mesoproterozoic heating event to widespread burial of the craton during Rodinia supercontinent assembly by sediments shed from the Namaqua-Natal orogen on the craton's margin. Later Neoproterozoic-Paleozoic erosion re-exhumed the basement to the surface. Spatial variability in ZHe data patterns can be explained by geologically-reasonable differences in Phanerozoic Karoo basin burial and erosion. The Mesoproterozoic and Karoo burial phases are analogous in that their detritus was derived from similarly-located orogens during two different supercontinent cycles. Mesoproterozoic deposition across the Kaapvaal craton may be part of a more global signal of burial and erosion during Rodinia assembly and breakup. Our dataset illustrates the power of THe and ZHe thermochronology for detecting missing Proterozoic depositional events in the rock record.