The organisation has started a consultation with staff about cutting jobs and has told the Department of Trade and Industry that more than 100 redundancies could follow.
The charity said the restructure would secure the charity's future and that redeployment and natural wastage would mean the actual number of redundancies would be "considerably fewer" than the total given to the DTI.
Rathbone has more than 800 staff and runs 70 training centres for disaffected young people in England, Scotland and Wales.
Rachael Maskell, national officer for the not-for-profit sector at trade union Unite, said it would be trying to prevent any redundancies.
"We have members at Rathbone and we are going to be fighting to protect their jobs," she said.
Richard Williams, chief executive of Rathbone, said the organisation needed to find a balance between the number of employees and the cash available.
"Rathbone plays a unique role in the learning and skills sector in the UK by meeting the education needs of highly disadvantaged young people, but we have to do that on a basis that is realistic in terms of balancing numbers, money and job roles," he said.
"The Government is strongly focused on getting young people, particularly the most disaffected, into work and training in order to improve their life chances.
"We want Rathbone to help deliver this challenge and need to make sure we are properly equipped to do so."