Aquino will meet Japanese Prime Minister Shinzo Abe during the one-day trip on June 24, in another move to deepen ties as the two nations have endured increasingly hostile disputes with China over rival maritime territorial claims.
The tensions will "likely" be a topic of discussion when the leaders meet, Aquino's spokeswoman, Abigail Valte, told AFP, although she did not want to give further details until an official agenda was determined.
In a statement announcing the trip last evening, the Philippine foreign ministry also indicated the China tensions would be discussed, while referring to a "strategic partnership" between the two nations.
Aquino will also deliver a speech on the Philippine government's efforts to end a decades-long Islamic insurgency in the south of the country, as it seeks to implement a peace pact with the Moro Islamic Liberation Front signed this year.
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Japan hosted secret talks between Aquino and MILF leader Murad Ebrahim in 2011, which later became recognised as a key moment in igniting the peace push.
Japan and the Philippines, former World War II enemies, have been drawn closer in recent years as they have tackled their parallel disputes with China.
Part of that equipment was a promise of 10 patrol boats for the Philippines' poorly-equipped coast guard, which is on the frontline of trying to monitor China's increasing presence in contested waters.
The dispute between the Philippines and China is over competing claims to parts of the South China Sea.
China claims nearly all of the sea, including waters close to the coasts of the Philippines and other claimant countries.
The Philippines has lodged repeated protests in recent years over China's growing military and civilian presence on islands and in waters within what it considers its exclusive economic zone.