The site will be owned by the charity's profit-making subsidiary, the Help for Heroes Trading Company, and will be rebranded as BmyHero in the next few days.
Bryn Parry, chief executive of Help for Heroes, said the charity's trading arm would fund the website, but declined to reveal how much money it was investing in it.
He said the site would remain commission-free for charities, which should carry on using it as normal, and would be run by the existing IT staff at Help for Heroes.
"Bmycharity did make a profit, but it lacked the investment to grow," Parry said. "We will provide the investment and the resources, and we are confident that it will be profitable in future."
Parry said that Help for Heroes was interested in developing some corporate partnerships for the site, but would not feature any adverts. Bmycharity has previously attempted to raise funds by charging firms to sponsor the site.
Banks give a small percentage of the charges made on online credit and debit card transactions back to website operators as a commission payment. It is understood this will be one way in which the site will be funded.