Records of geomagnetic field variations from continental Africa are sparse yet provide a key dating tool for low‐latitude paleoclimatic changes. Long‐lived tectonic and crater lakes in eastern tropical Africa potentially provide important, long (>100,000 years, kyrs) and continuous sedimentary records of African monsoonal climate over past glacial and interglacial stages; the environmental backdrop to human evolution and dispersion. Here, notwithstanding its low latitude location, we present a detailed paleomagnetic record from eastern equatorial Africa extracted from the upper ∼129 m of a continuous sediment sequence drilled in Lake Chala (3°S; 37°E), a permanently stratified crater lake near Mt. Kilimanjaro. The high and stable sedimentation rate (∼0.85 m/kyr), lack of compaction and reliable paleomagnetic signal (assessed by paleo‐ and rock magnetic analyses) enabled the production of a new virtual geomagnetic pole (VGP) record for the last ∼150 ka for equatorial Africa. Six magnetic excursions are recorded: Blake 1 and 2, Post‐Blake, Laschamp, Mono Lake and Hilina Pali. This exceptional record provides key information on the recurrence and duration of intervals of Quaternary geomagnetic instability, and independently‐obtained constraints on the Hilina Pali excursion. Our new paleomagnetic record thus provides a reference data set for late‐Quaternary geomagnetic excursions from African sites and a basis for better understanding of the temporal and spatial evolution of Earth's magnetic field. Finally, correlated with a revised geomagnetic instability timescale, these excursions provide a robust, independent age model for the Lake Chala sediment record, critical for correlating its paleoclimate and environmental proxy records to global reference records.