The $5m (£3.2m) award is given each year to an elected leader who governed well, raised living standards and then left office.
But the previous award was the fourth in five years to have gone unclaimed.
Mr Pohamba, a former rebel who fought for his country’s independence, has served two terms as Namibian president.
He was first elected in 2004, and again in 2009. He is due to be succeeded by President-elect, Hage Geingob.
Salim Ahmed Salim, the chairman of the committee that awarded the prize, said that under Mr Pohamba, Namibia had cemented its reputation as “a well-governed, stable and inclusive democracy with strong media freedom and respect for human rights”.