Tatsumi Kimishima, the current head of human resources, will take on the new role from Wednesday after former president Satoru Iwata died of cancer in July.
Kimishima takes the reign of the Japanese gaming giant, known for its iconic Super Mario character, as the company tries to re-establish itself as a leading console brand in the face of stiff competition from Sony's PlayStation 4 and Microsoft's Xbox One, as well as mobile gaming.
"They are in a vulnerable position," Heloise Thomson, analyst at Enders Analysis, told CNBC by phone.
"From a brand perspective, they have a golden brand. But you can't survive off nostalgia and they haven't done enough in marketing in international markets to tell people what Nintendo is right now."