Although the exact length of the deal was not revealed, it has been widely reported to be a 10-year contract worth as much as £150million if McIlroy, previously with Titleist, goes on winning majors.
McIlroy will use Nike's full range of clubs, balls, clothing and accessories, with the clubs used competitively for the first time in the Abu Dhabi HSBC Championship later this week against a field including the other leading golf name in Nike colours, 14-major winner and world number two Tiger Woods.
"I chose Nike for a number of reasons," McIlroy said. "It's a company and a brand that really resonates with me. It's young. It's athletic. It's innovative. They are committed to being the best, as am I.
"Signing with Nike is another step towards living out my dream."
Cindy Davis, president of Nike Golf, added: "Rory is an extraordinary athlete who creates enormous excitement with his on-course performance while, at the same time, connecting with fans everywhere.
"He is the epitome of a Nike athlete and he is joining our team during the most exciting time in Nike Golf's history. We are looking forward to partnering with him to take his remarkable career to the next level."
McIlroy won his first major at the 2011 US Open by eight shots, and repeated the winning margin at the USPGA Championship last August.