Michelle Obama met Japan's first lady Akie Abe in Tokyo on the second day of her five-day trip to Japan.
The Obama administration launched "Let Girls Learn" programme two weeks ago to expand its effort to help adolescent girls worldwide attend and complete school.
The US first lady's five-day trip starting Wednesday to Asia is focusing on helping about 62 million girls around the world, half of whom are adolescent, to go to school, Xinhua news agency reported.
"Today we are pleased to announce that the United States and Japan will partner in this critical area, elevating the issue of girls' education on their shared development agenda," said the first lady.
"With this new partnership between our two nations, we are issuing a call to action to nations around the world."
As one of the largest economies in the world, the US will allocate $250 million in new and reallocated funds in support of the "Let Girls Learn" programme in its fiscal year 2016 Budget.
Japan will commit Official Development Assistance in excess of 42 billion yen ($340 million) over three years starting from 2015 for girl's empowerment and gender-sensitive education.
Michelle Obama's visit to Japan comes ahead of Japanese Prime Minister Shinzo Abe's visit to the US a month later. She will travel to Kyoto on March 20 and leave for Cambodia on the same day.