The new charity will be known as Impetus – the Private Equity Foundation. The merger is likely to be completed by the end of March.
Shaks Ghosh, chief executive of the PEF, will step down at that point, and Daniela Barone Soares, chief executive of Impetus, will continue as the chief executive of the new, merged organisation.
Johannes Huth, chair of the PEF, will chair the new organisation. Louis Elson, chair of Impetus Trust, will be vice-chair.
The Impetus Trust has an annual turnover of about £5.9m and about 25 staff; the PEF has a turnover of about £5m a year and 13 staff.
Both organisations operate models that combine grants, volunteer work by high-level professionals, such as investment professionals and management consultants, and in-depth support for charity senior management teams.
The combined charity will continue to be based in London and will move to new offices.
Soares said the two organisations had similar goals and philosophies. There were no plans for redundancies and no plans to cut any services as a result of the merger, she said.
Both charities were in strong financial positions and were growing fast, said Soares, but conversations between the two chairs had led them to conclude that they could achieve more together.
"We had both advised others to merge from a position of strength, and we decided to take our own advice," she said.
Soares said that Ghosh, who became founding chief executive of the PEF six years ago, had a positive attitude to the idea of merger and saw it as an opportunity.