El Al Israel Airlines says it will operate three round trips a week from March 2020 connecting the two cities. The flight time will be about 12.5 hours.
The announcement comes as the two countries increase exchange of goods and services.
Bilateral trade rose 30 percent over the past five years to about 3.7 billion dollars.
More than 20,000 people in Japan visited Israel last year as the country has grown to become a hub for high tech companies.
40,000, mainly tourists, came to Japan from Israel during the same period.