Sixteen of the 17 independently constituted Brook sexual health charities have voted to become one organisation.
The new organisation will have an income of £15m and employ hundreds of staff. Jobs could be lost when the change takes effect in March, however.
Simon Blake, the national director of Brook, said sexual health services had changed considerably since the charity was founded in 1964 and the move would reduce inconsistencies among regional organisations.
He said it would make Brook "bigger, bolder and better", help it to achieve its goal of doubling the number of people it reaches by 2018 and "reduce duplication of costs".
But he said it was too soon to say how many of the 660 full and part-time staff employed by Brook could lose their jobs.
Regional trustee boards are being dissolved and a new eight-person national board, chaired by Eve Martin, has been appointed.
"The decision to become one organisation has been driven by an absolute focus on the needs of young people and how Brook best protects and promotes their sexual health," said Martin.
Brook Northern Ireland is the only Brook charity that has not yet agreed to join the new structure.
Mary Crawford, its director, said it was still trying to decide the best way forward and that it was not in dispute with the national body.