The cornea is a specialized component of the vertebrate eye that provides protection, refractive power, transparency for optical imaging and mechanical support. However, the corneas of birds have received little attention with no comprehensive study of their functional morphology. Using light microscopy and both scanning and transmission electron microscopy, the first description of the ultrastructure of all of the main components of the cornea in two different‐sized individuals of the Little Penguin Eudyptula minor is presented. Two types of microprojections protrude from the surface of the cornea with a predominance of microridges and microvilli found in central (flattened) and peripheral regions, respectively. Epithelial cell density is higher in peripheral cornea, especially in the larger (older) individual, while there is a reduction of epithelial cell density with age. The cornea comprises a thick epithelium uniquely attached to the basement membrane with numerous incursions rather than anchoring fibres and anchoring plaques as is found in other vertebrate corneas. Posterior to Bowman's layer, the orthogonally‐arranged collagen fibril lamellae in the stroma form extensive branches and anastomoses. Desçemet's membrane is well‐developed with an anterior or foetal portion with long banding. However, the thickness of Desçemet's membrane is larger in the older individual with the inclusion of an additional irregular pale‐staining posterior portion. Polygonal endothelial cells extend across the cornea as a monolayer with often tortuous cell junctions. Endothelial cell density increases towards the periphery, but decreases with age. Primary cilia are observed protruding through the central region of some endothelial cells into the anterior segment but subsurface structures resembling cilia suggest that these features may be more common. The ultrastructure of the corneal components reveals a range of functional adaptations that reflect the amphibious lifestyle of this seabird.