Denis Mukwege, 53, who runs a clinic in Bukavu, has said all sides have "declared women their common enemy".
He says his award from the Nigerian Daily Trust paper of $20,000 (£13,700) will be used to fund a centre to help rape victims rejoin society.
His clinic receives an average of 10 new patients every day.
Women in DR Congo are often raped and subjected to terrible violence by armed men as part of the decade-old conflict.
The Panzi hospital helps women with the physical and psychological injuries after being attacked.
It also provides help for women who have contracted HIV/Aids from their attackers.
A third of patents undergo major surgery.
"I am pleased to accept this award if it will highlight the situation of women in eastern Democratic Republic of Congo," Dr Mukwege told the BBC French service after accepting the award at a ceremony in Nigeria's capital, Abuja.Dr. Mukwege's work illustrates the plight of women in war-torn countries, whose bodies literally become part of the battleground. Women are raped and otherwise violated as a tool of war, and their experiences deserve to be treated as war crimes.
In her confirmation hearing for Secretary of State, Hillary Clinton said the following when Barbara Boxer asked her about slavery and trafficking of girls and women:
We hope that, as individuals, we all recognize the same sentiments.
I want to pledge to you that as secretary of state I view these issues as central to our foreign policy, not as adjunct or auxiliary or in any way lesser than all of the other issues that we have to confront.
I, too, have followed the stories that are exemplified by the pictures that you held up. I mean, it is heartbreaking beyond works that, you know, young girls are attacked on their way to school by Taliban sympathizers and members who do not want young women to be educated. It's not complicated: They want to maintain an attitude that keeps women, as I said in my testimony, unhealthy, unfed, uneducated.
And this is something that results all too often in violence against these young women, both within their families and from the outside. This is not culture. This is not custom. This is criminal. And it will be my hope to persuade more governments, as I have attempted to do since I spoke at Beijing on these issues, you know, 13 and some years ago, that we cannot have a free, prosperous, peaceful, progressive world if women are treated in such a discriminatory and violent way.
If you would like to hear Dr. Mukwege speak locally, he will be appearing in conversation with Eve Ensler at the Carter Center on Feb. 23. Visit their website for tickets.