Parkes, who has worked for the BHF since March 2011, will start at the children’s charity in January.
Her new role will include responsibility for the charity’s 600-strong chain of shops, its commercial services arm and its fundraising teams.
Javed Khan, chief executive of Barnardo’s, said Parkes would bring great experience and skills to the charity.
Parkes said: "I am looking forward to being a part of the new ambitious strategic plan and growing income for Barnardo’s to help transform the lives of more children and their families.
"It has been a really difficult decision for me to leave because the BHF is such an incredible organisation.
"It has been an absolute privilege to work with so many talented and inspirational colleagues.
"I wish the BHF every success in delivering its strategy to 2020, whilst looking forward to the new and exciting challenges at Barnardo’s."
Simon Gillespie, chief executive of the BHF, said Parkes had made a huge contribution and wished her all the best in the new role.
A BHF spokeswoman said recruitment was already under way for an interim director of fundraising.