Initially described as member of Anseriformes within Galloanserae, the definitive taxonomic position of Vegavis was debated among paleontologists over two decades until the 2025 description of a nearly complete skull, discovered in 2011, supported its original classification.

[3] The specimen, cataloged as MLP 93-I-3-1, was found in 1993 from the López de Bertodano Formation at Cape Lamb on Vega Island, Antarctica, and was first thought to be an indeterminate presbyornithid.

[8] After 20 years since the formal naming of Vegavis, a nearly complete skull specimen (AMNH FARB 30899) discovered by Eric M. Roberts in 2011 from the López de Bertodano Formation was officially described in 2025.

[14][15] In a 2025 study which described a nearly complete skull of Vegavis, Torres et al. supported its placement within crown group Anseriformes, sister to Conflicto and Anas, based on their revised phylogenetic analyses.

[9] Agnolín et al. (2017) proposed the family Vegaviidae as stem-group Anseriformes containing Vegavis, Polarornis and several other extinct avian genera,[16] but the monophyly of this clade was questioned by subsequent studies.