High-precision U–Pb ion microprobe analyses provide new constraints on the emplacement and origin of the Kinabalu granite in Sabah, northern Borneo. The granite is a sheeted laccolith-like body comprising dyke-fed granitic units that young downwards, each emplaced beneath the previous sheet. Analyses of concentric growth zones in zircons indicate crystallization between 7.85 ± 0.08 and 7.22 ± 0.07 Ma, and show that the entire pluton was emplaced and crystallized within less than 800 ka. Several pulses of magmatism are recognized, each lasting for a maximum of 250 ka, and possibly as briefly as 30 ka. The oldest ages coincide with the highest elevations whereas the youngest ages are found at lower elevations around the edge of the body. Based on these new age data and field observations we identify the biotite granodiorite, hornblende granite and porphyritic facies as the Upper, Middle and Lower Units respectively. Inherited zircon ages indicate different protoliths for the Upper and Middle Units. The Upper Unit is derived from attenuated continental crust of the South China margin subducted beneath Sabah. The Middle Unit is sourced from melting of the crystalline basement in Sabah with little or no contribution from South China crust.