Kimishima, who is currently the head of human resources, will take office on Wednesday, the company said in a press release.
The 65 year-old former banker also served as CEO of Nintendo America between 2006 and 2013.
The Kyoto-based company said it has named Kimishima in order to "reinforce and enhance its management" after the death of its CEO Satoru Iwata.
Iwata died in July at the age of 55, just months after abandoning a controversial consoles-only policy and launching a push into the booming smartphone games market.
A leading figure in the videogame industry, Iwata oversaw the success of Nintendo's Wii games console and a surge in revenue before smartphone games started eating away at its success.
A visibly thinner Iwata announced last year that he was sick and did not attend the firm's shareholder meeting in June 2014, although the severity of his illness was unclear at the time.
He returned to work over the following months, and continued to be the public face of Nintendo, including when the company announced financial results in May.
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