The 11-day annual exercise, to kick off on May 2 in waters off Thailand, will focus on international disaster relief operations in the wake of the Indian Ocean tsunamis.
Japan's military, known as the Self-Defense Forces, has participated as an observer since 2001, amid concern in neighboring countries about Japan's past militarism.
"Japan will formally participate in the drill for the first time," Defense Agency Director-General Yoshinori Ono told a news conference. "It is good to share experiences in disaster relief."
It marks the first time Japan is participating in multilateral military exercises it did not have a central role in organizing, a Defense Agency official said. Cobra Gold has been held since 1982.
Under the plan, Japan will send 25 personnel from the air, ground and maritime forces to join the exercise starting the northern city of Chiang Mai.
Last year the exercises had five participants -- the United States, Thailand, the Philippines, Singapore and Mongolia -- with 10 observer nations including Japan, China, South Korea, India and Australia.
China and South Korea this month have seen passionate anti-Japanese street protests after Tokyo approved a history textbook which allegedly whitewashes atrocities committed by Japan when it invaded neighboring countries.
But Japan saw little opposition earlier this year when it mounted its biggest military operation since World War I -- sending 950 troops to Indonesia for tsunami relief.
Japan also has 600 troops posted in Iraq, the first time Tokyo has sent troops to a country at war since it renounced war in its US-imposed 1947 constitution.