The Napier Complex of Enderby Land and Kemp Land is a unique part of the Eastern Antarctic Shield, as it preserves history of crustal growth extending from the Eo- to Neoarchean. It is composed mainly of enderbitic and charnockitic gneisses and granulites metamorphosed at ca. 2.5 Ga, and locally at ca. 2.8 Ga, under high- to ultra-high temperature conditions. These events have been well-characterized in the central and western parts of the complex; however, the south-southwestern region has been little studied. Samples from the southern Scott and Raggatt Mountains were selected for zircon U-Pb dating by Secondary Ion Mass Spectrometry and whole-rock geochemical analysis. Tonalitic gneiss from the Raggatt Mountains and trondhjemitic gneiss from the southern Scott Mountains have protolith ages of 2711 ± 5 Ma and 2726 ± 6 Ma, respectively. In contrast, tonalitic samples from the southern Scott Mountains have protolith ages of ca. 2539 ± 5, 2533 ± 5 and 2522 ± 9 Ma. The younger generation of magmatism overlaps the timing of metamorphic zircon growth between 2540 and 2440 Ma observed in this study. The geochemistry of ca. 2720 Ma gneisses indicates that magmatism was generated by medium-pressure melting (>1.5 GPa) of basaltic crust, whereas ca. 2530 Ma magmas were generated at lower pressures (<1.2 GPa). The ca. 2.7 Ga magmatism may be associated with continental crust formed at 2.8 Ga, or be newly formed crust that was assembled with older prior to or during a tectonometamorphic event at ca. 2.5 Ga. Tonalitic magmatism at 2.53 Ga during the first half of the 2585–2420 Ma metamorphic event may be a product of partial melting during high-grade metamorphism. Although protolith ages across the complex are still scarce, differences between regions raise the possibility that the complex contains crustal domains of different ages and origins that may not have been assembled until the ca. 2.5 Ga tectonothermal event.