As part of the deal, the Family and Childcare Trust has changed its name to Coram Family and Childcare, and will be based at Coram’s offices in London.
The chief executive and finance officer roles at the Family and Childcare Trust will be made redundant as part of the move, which is expected to be legally formalised on 1 August.
But Ellen Broome, chief executive of the Family and Childcare Trust, will provide "transitional leadership" to help with the move to Coram, a spokeswoman for the Family and Childcare Trust said.
No other redundancies are expected, the spokeswoman said.
The spokeswoman was unable to confirm the number of staff employed by the Family and Childcare Trust, but its accounts for 2016/17 show it had an average of 25.5 employees over the course of the year.
The Family and Childcare Trust’s annual income has roughly halved since 2012/13 to £1m in the year to the end of March 2017, figures on the Charity Commission’s website show.
Spending has significantly outstripped income in each of the past five years, the accounts show, with the charity recording a total deficit of £4.5m in the five years between 2012/13 and 2016/17.
The spokeswoman said the charity was joining Coram to share the group’s infrastructure and expertise, and would remain an independent charity.
The board, branding and leadership of Coram will not change as a result of the merger, the spokeswoman said.
Broome said: "I am very excited by the opportunity that joining the Coram group provides to help us meet the needs of more families and have a greater impact.
"Many parents in the UK are frozen out of work by the high cost and low availability of childcare, and many children miss out on the boost to their outcomes that high quality provides. The brunt of childcare costs and shortages are borne by disadvantaged families.
"I look forward to working as part of the Coram group to create a childcare and early years system that works for all families."
Dr Carol Homden, chief executive of Coram, said: "Tackling inequality and making sure that all children are respected and protected are at the heart of Coram’s work, and Coram Family and Childcare will help us to have a greater impact for families.
"By combining expertise and experience, we will develop, deliver and promote best practice to strive for change and will not rest until every child has the best possible chance in life."