It is looking to raise more than $900m (Â£624m) from investors, which would value the firm at more than $5bn.
The listing, planned for July, could make it the world's biggest technology initial public offering this year.
Line is looking to raise funds to expand into the US and help it compete with rivals such as Facebook Messenger, WhatsApp and China's WeChat.
The app first made its debut in 2011 and is the most popular messaging service in Japan, Thailand and Taiwan.
It is famous for selling animated stickers and stamps that people can share while chatting. Line also provides free voice calls and services such as music streaming.
Line's management have looked to take the company public for several years now. It submitted an IPO application to the Tokyo Stock Exchange in 2014.
However, those plans were shelved at the time due to weak global markets.
Line had 218 million monthly active users at the end of March.
Japanese phone messaging app operator, Line, has said it plans to list its shares in both Tokyo and New York.