There she met with hospital workers and patients, including women recovering from the physical and psychological effects of rape.
"Heal Africa is doing amazing work," said the Secretary of State, who is on a seven-country tour of Africa.
It is estimated that 200,000 women and girls have suffered sexual violence in the east of the Democratic Republic of Congo since 1996 and 400 new cases are registered every month.
Heal Africa's hospital in Goma runs operating theatres which specifically treat women and girls who have been injured in the course of such attacks. Counselling is provided to assist their emotional and spiritual recovery and legal aid is also offered to help those seeking justice against their attackers.
Often women who have been raped find themselves ostracised afterwards by their families and therefore economically vulnerable. Heal Africa also runs a skills training programme to enable them to make a living.
Sadiki Byombuka, Tearfund's representative in DR Congo, said: "What is very interesting is Heal Africa's integrated approach to the gender and sexually based violence situation in North Kivu.
"It comprises of medical treatment, psychosocial counselling, social and livelihoods support, advocacy for justice for the victims and community social reconstruction for complete and deep healing. That is why Tearfund supports the work of Heal Africa and other like-minded partners in the DRC."
The army of the Democratic Republic of Congo has been involved in a long conflict with various rebel groups operating in the east of the country. Although some groups have been driven out in recent months, ongoing fighting continues to lead to the displacement of more families.
Mrs Clinton made a point of going to North Kivu to highlight her concern about attacks on women and rape being used as a weapon of war.
"The atrocities that so many have suffered distils evil into its most basic form," she told reporters. "Those who attack civilian populations using systematic rape are guilty of crimes against humanity."