The £179 million ($271 million, 211 million euros) fund will provide essential healthcare in an effort to bring peace, Hague said during a visit to the conflict-riven east of the country.
"As we have travelled around the area, I have been struck not only by the human cost of these crimes but also by the limited facilities and resources available to support survivors," Hague said.
"As part of the work I am championing to tackling the culture of impunity for sexual violence in conflict I have announced project funding to help increase capacity for investigating sexual violence crimes."
The assistance was "essential to help create sustainable peace and security in DRC", he added.
The British programme will operate across 10 percent of the country, rebuilding clinics, training health staff, supplying medicines and equipment, and improving water and sanitation.
Hague's visit is part of a British initiative to agree new international action to prevent the use of rape and sexual violence as a weapon of war.
Hague has called on the G8 to agree that rape and sexual violence constitute breaches of the Geneva Conventions governing warfare.
International development minister Justine Greening said the initiative would improve health services and supply essential medicine and equipment.
The programme will supply contraception, vaccinate 64,000 children against measles each year and distribute anti-malarial bed-nets to pregnant women and young children.
Hollywood actress Angelina Jolie on Monday joined Hague on his visit in a bid to encourage world powers to do more to tackle rape and sexual assault in war zones.
Their trip to central Africa, which began in Rwanda, is aimed at forcing the Group of Eight world powers to address the issue more seriously.
Hague said he would be making the issue his priority when he hosts the annual meeting of G8 foreign ministers next month in London.