Palaeognaths, the sister group of all other living birds, were long considered to be relics from the breakup of the Gondwanan supercontinent. However, there is renewed skepticism of the extent to which vicariance explains palaeognath biogeography, with recent molecular studies instead arguing for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing the evolutionary relationships and timing of divergence among this group, which remain contentious. Recently, mitogenome sequences from the extinct elephant birds of Madagascar have further informed the palaeognath phylogeny; however, nuclear loci have been unavailable due to the rarity of bone specimens with well-preserved ancient DNA (aDNA). Nevertheless, nuclear information often proves crucial for accurately recovering deep evolutionary relationships. Here, we use DNA extracted from fossil eggshell in conjunction with target enrichment and next-generation sequencing techniques to independently reconstruct the mitochondrial genome and recover nuclear loci from Aepyornis sp. We confirm that elephant birds are sister taxa to the kiwi (Apteryx spp.); however, our data suggests that, like neognaths, the notopalaeognathae (all palaeognaths excluding ostrich) underwent an explosive radiation between 64.2-54.2 mya—well after the break-up of Gondwana, and more rapidly than previously estimated from mitochondrial data alone. These results further support the idea that ratites convergently evolved flightlessness immediately following the K-Pg mass extinction event, favoring the dispersal hypothesis over a vicariant model. Our study reinforces the importance of including information from the nuclear genome of extinct taxa for understanding the evolutionary history of their modern relatives. With approximately 3% endogenous aDNA retrieved, avian eggshell can be a valuable substrate for recovering high quality aDNA, particularly from environments that are not typically conducive to aDNA preservation. We suggest that elephant bird whole genome recovery is ultimately achievable, and will provide future insights into the evolution, adaptation, and development of these enigmatic birds.