A spokeswoman for the charities said the new organisation, whose new name will be announced at a later date, will be legally merged from January.
She said the merger came about because of the similarities between the two charities. By joining together, she said, both charities hoped they would have a bigger impact on reducing the prevalence of bowel cancer, and would eventually help to eliminate it.
There are no financial motives behind the merger, she said, with the charities having similar levels of income: Bowel Cancer UK had an income of £2.3m in 2016; Beating Bowel Cancer had an income of £1.7m in the 2016/17 financial year.
The charities have 65 employees combined, about half of which come from each charity, and all will be transferred to the new organisation.
The chief executive of the new charity will be Deborah Alsina, chief executive of Bowel Cancer UK, with Beating Bowel Cancer’s interim chief executive, Judith Brodie, ending her temporary role with the charity next month.
Brodie took over from Mark Flannagan, who stood down in March after six and half years in the role.
The charity’s new board will have 15 trustees and will feature individuals from both existing boards. It will be chaired by Patrick Figgis, a trustee at Beating Bowel Cancer.
The charities currently have headquarters in Teddington in west London and London Bridge, but will find new offices when the leases for both buildings expire next year.
Other staff based regionally across the UK will be unaffected by the transfer to a new headquarters, the spokeswoman said.
Figgis said: "Both boards of trustees unanimously welcome this merger as the best opportunity to achieve our shared vision of a world where no one dies of bowel cancer. As a board we will support the establishment of an ambitious but achievable strategic plan to help us deliver our purpose and realise our ambition. We already have exciting plans for 2018, including awarding our first research grants and digital development of our patient and carer services."
Alsina said: "Bowel Cancer UK and Beating Bowel Cancer are joining together because we are not prepared to wait for change to happen, and we are determined to drive it forward so lives can be saved."