The skull is from a penguin that lived in New Zealand over 60 million years ago during the Paleocene epoch. It likely lived much like penguins today, researchers said.
But while today's penguins have been diving instead of flying for tens of millions of years, the change was relatively new for the ancient penguin.
"It is the oldest [penguin] following pretty closely after the loss of flight and the evolution of flightless wing-propelled diving that we know of," said James Proffitt from University of Texas in the US.
They thought that loss of flight would impact brain structure - making the brains of ancient penguins and modern penguins similar in certain regions.
However, after analysing the endocast and comparing it to modern penguin brain anatomy, no such similarity was found, researchers said.
The brain anatomy had more in common with skulls of modern relatives that both fly and dive such as petrels and loons, than modern penguins.
"What this seems to indicate is that becoming larger, losing flight and becoming a wing-propelled diver does not necessarily change the [brain] anatomy quickly," said Proffitt.
"The way the modern penguin brain looks does not show up until millions and millions of years later," he said.
However, similarities in the brain shape between the ancient species and diving birds living today suggest that diving behaviour may be associated with certain anatomical structures in the brain, researchers said.
The findings were published in the Journal of Anatomy.
