The program, which begins in July, will tap in U.S.-based company Techstars, a firm with more than 1,000 firms with a combined market cap of $9.6 billion in its accelerator portfolio.
A total of 10 start-ups will be selected from around the world for Rakuten's program, which will focus on messaging technology.
The shortlisted companies will receive an initial investment of $120,000 each, coming jointly from Rakuten and Techstars. They will also receive guidance from top executives at Rakuten and access Techstars' wide network of founders, alumni and mentors.
"It's a very good initiative to empower the entrepreneurs and (bring) innovation to society," Hiroshi Takasawa, CEO at Rakuten Asia's regional head office and head of the company's investment arm, told CNBC.
The executive said Rakuten could further invest into any of the 10 start-ups if they show promise.
Rakuten is still deciding on selection criteria for the start-ups.
Applications for the accelerator program is set to open on Jan. 8, 2018.