Kainos will be a subsidiary of Langley House under the new structure, which took effect on 1 October, and will maintain its identity and continue to run its contracts.
Tracy Wild, chief executive of the Langley House Trust, a Christian charity founded in 1958, has also become chief executive of Kainos, which was established in 1999.
She replaces Phil Edgington, chief executive of Kainos, who is retiring. A Langley House spokeswoman said there had been no redundancies as a result of the merger.
Langley House has more than 200 staff at sites across England and a turnover of about £8m a year. It works in the community to rehabilitate ex-offenders and those at risk of offending.
Kainos has 12 staff and an annual turnover of about £500,000. It has runs community projects and works in prisons to help offenders live crime-free lives after they are released.
Negotiations began earlier this year, when Edgington and trustees of Kainos approached Langley House to discuss a merger.
A Langley House spokeswoman said the two sides felt they would be strengthened by combining their expertise and there were no financial difficulties driving the merger.
In a statement, Wild said: "We are delighted by the prospect of working more closely with Kainos Community and can see benefits for both organisations.
"I can see how our combined talents – as shown by the highly credible results that both charities have achieved in their own right – will produce exciting new developments in the future, such as a comprehensive pathway of support for offenders from inside prison through to successful independence in the community."