This study seeks to demonstrate the relationship between magnetic anomalies and geological structure of Precambrian complexes of the Bunger Oasis and Highjump Archipelago, East Antarctica. Aeromagnetic data effectively maps geological units, revealing distinct magnetic signatures for Neoarchean and Palaeo Mesoproterozoic terrains. This provides the possibility of significantly improving existing geological maps, particularly in poorly mapped areas like the Highjump Archipelago. Magnetic anomaly intensity and strike correlate with rock composition and regional structural trends, enabling better differentiation of lithological units like magnetic metapelites and non-magnetic metapsammites. Tilt derivative calculations enhance structural mapping by linking magnetic sources to specific rock suites. As an example, a prominent northeast-striking belt of positive magnetic anomalies marks a key boundary between Archean and Mesoproterozoic complexes. Variations in the belt’s strike suggest complex tectonic history, including potential fault contacts. Intrusive bodies exhibit complex magnetic characteristics. The Paz Cove intrusion displays a negative anomaly likely due to reversed remanent magnetization, while the Algae Lake intrusion has both positive and negative anomalies reflecting varying rock compositions. The Gabbro intrusions in the northeastern part of the Highjump Archipelago correlate with positive anomalies, while the intense negative anomaly over the Kashalot Island gabbroic intrusion suggests reversed magnetization. This study aims to produce a structural (tectonic) map of the Bunger Oasis and Highjump Archipelago by analyzing magnetic anomaly data collected by an unmanned aerial vehicle during the 69th RAE, combined with existing geological information for the area. The study highlights the value of UAV aeromagnetic surveys for detailed geological mapping in challenging environments, providing crucial insights into East Antarctica’s Precambrian history.