The Japanese games maker will launch gaming app Super Mario Run.
The announcement was made on stage at an Apple event where boss Tim Cook also revealed its newest device, the iPhone 7.
The game will launch this year, though no specific date was given.
Nintendo has until now avoided jumping on the popularity of smartphones, sticking with its own platforms.
Pokemon Go was Nintendo's first foray into the world of mobile gaming and shares rocketed after people went crazy for it. It was, however, developed with other companies and Nintendo will have to share the profits and admitted the impact on its earnings will be "limited".
Shares in Nintendo spiked nearly 13 per cent on the Apple announcement.