Uranium-lead dating of apatite was undertaken by Laser Ablation-Sector Field-Inductively Coupled Plasma Mass Spectrometry (LA-SF-ICPMS) in situ on apatite from principal rock types of the Loolekop phoscorite-carbonatite intrusion within the Phalaborwa Igneous Complex, South Africa. In situ U-Pb analysis on selected apatite produces U-Pb ages of 2 083.9 ± 41.9 Ma (n = 33; MSWD = 0.87), 2 020.4 ± 116.7 Ma (n = 18; MSWD = 0.91) and 2 034.3 ± 39.0 Ma (n = 17; MSWD = 0.6) for phoscorite, banded carbonatite and transgressive carbonatite, respectively, with a combined age of 2 054.3 ± 21.4 Ma (n = 68; MSWD = 0.86), which we interpret to indicate the timing of emplacement. Apatite U-Pb dates are similar to dates reported in previous studies using zircon and baddeleyite U-Pb systems from the same rock types, showing that apatite can be used as geochronometer in the absence of other commonly used U-Pb-bearing accessory minerals, not only in carbonatite-phoscorite complexes, but in all mafic igneous intrusions. Similar ages for zircon, baddeleyite and apatite indicate little to no re-equilibration of the latter, and suggest that the Loolekop Pipe intrusion cooled below 350°C within ~21 Ma of emplacement. This conclusion is supported by apatite BSE images and trace element systematics, with unimodal igneous trace element characteristics for apatite in each sample. The combination of in situ U-Pb geochronology, trace element geochemistry and BSE imaging makes apatite a useful tool to investigate the emplacement mechanisms of carbonatite-phoscorite complexes, which is particularly advantageous as apatite is one of the main mineral phases in these rock suites.