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.

The hardware retailer's fourth quarter sales rose 9.5% to almost $21bn (Â£14.9bn) between November and January compared with the same period in the previous year.
The company has benefited from pent-up demand in the housing market.
On Tuesday the National Association of Realtors reported existing home sales rose by 0.4% in January - on top of a 12% surge in sales in December.
Low interest rates, combined with growth in the job market and wage increases, have bolstered the US housing market, but fears of slowing global growth could dampen confidence this year.
Home Depot sales were also helped by unusually warm winter that has allowed more people to continue home improvement projects throughout the winter.
Like-for-like sales rose 8.9% - far higher than analysts' estimates of 5.3% growth.
The higher sales resulted in Home Depot posting a profit of $1.47bn for the fourth quarter, higher than the $1.37bn for the same period in 2014/15.
Shares of Home Depot rose 2% in afternoon trading in New York.
The company also announced it would increase its quarterly dividend by 17% and conduct a $5bn share buyback this year.
Despite the recent gains, the outlook for the US housing market in 2016 remained uncertain.
The National Association of Realtors said that housing inventory fell by 2.2% from last year, leading to higher prices. The median existing home price was $213,800 across the US, up 8.2% from January 2015.
"The spring buying season is right around the corner and current supply levels aren't even close to what's needed to accommodate the subsequent growth in housing demand," said Lawrence Yun, the association's chief economist.
"Home prices ascending near or above double-digit appreciation aren't healthy - especially considering the fact that household income and wages are barely rising," he added.

The Marchwood Park and Cracknore Hard industrial estates, covering 113.73 acres, were acquired by Associated British Ports (ABP) for an undisclosed amount.
Port director Nick Ridehalgh said the estates would provide "strategic long term value" for the company.
Local councillor David Harrison called for a "statement of intent" from ABP.
The estates are located on the western side of Southampton water, opposite the cruise terminal and Southampton Docks, and are six miles (9.5km) from the M271 motorway.
The sites had been owned by Oceanic Estates for the last 15 years and and are among the largest self-contained industrial and warehouse holdings in the South East with occupiers including Ocado and Royal Mail, according to property consultants Lambert Smith Hampton.
Mr Harrison, who represents Totton South and Marchwood, said: "In the longer term, local people in Marchwood and Totton South will be particularly concerned about any change to future usage of the site. For example, any increases in traffic and more pressure on our overburdened local roads will be completely unacceptable".
Mr Ridehalgh said: "Our intention is to continue to develop the estates to increase the income... and directly contribute to the economic success of the Port of Southampton and the wider region."
Japanese phone messaging app operator, Line, has said it plans to list its shares in both Tokyo and New York.
[NEXT_CONCEPT]
Home Depot has reported better than expected sales growth, helped by a strong US housing market.
[NEXT_CONCEPT]
The company which manages Southampton port has bought industrial estates close to its western side.