(U‐Th)/He data were obtained for four minerals (baddeleyite‐BHe, titanite‐THe, zircon‐ZHe, apatite‐AHe) from the 2.06 Ga Phalaborwa carbonatite complex and nearby Archean basement of the Kaapvaal craton, South Africa. Our goals are to evaluate the relative He temperature sensitivities of these phases, better understand how radiation damage and other factors affect them, and inform aspects of the craton's thermal history. BHe dates overlap with Phalaborwa emplacement and record the highest temperatures of the dated phases. THe dates are 700–1,100 Ma and display a limited negative date‐eU correlation. ZHe dates are negatively correlated with eU, are younger (561–32 Ma) and have higher eU than the THe data, with the highest‐eU grains younger than the AHe dates. AHe dates are reproducible with a mean of 107 ± 7 Ma. The THe and ZHe data show radiation damage reduction of their He retentivities manifested as the negative date‐eU correlations. Alpha dose estimates for zircon are several orders of magnitude higher than for titanite, consistent with the ZHe dates recording lower temperatures and a younger portion of the history than the THe dates. Thermal history modeling yields time‐temperature paths that (1) explain the AHe, ZHe, and THe data while honoring existing geologic constraints, thus demonstrating the internal consistency of the data set, (2) imply possible reheating during Namaqua‐Natal orogenesis, and (3) limit maximum probable temperatures to ∼180°C during 300–183 Ma Karoo basin burial. The results show that exploiting multiple (U‐Th)/He thermochronometers and radiation damage effects can provide new insights into long‐term craton evolution.