Yolanda Becerra, Chairman of Organizacion Femenina Popular, received the 200,000 kronor (US$31,636; Ђ21,590) Per Anger Prize from Swedish Crown Princess Victoria at a ceremony in Stockholm.
The organization was recognized for "tirelessly working in a threatening environment to defy the force of arms and strengthen voices that are at risk of suppression."
"By giving an international award to an organization which is working under threats we hope that the pressure on OFP, their more than 3,000 members and other human rights organizations in Colombia, will ease," said Lise Bergh, General Secretary of Amnesty International, Sweden.
OFP started in 1972 with a soup kitchen for the poor and has expanded to include legal assistance and support for young people.
The organization's headquarters are in the city of Barrancabermeja, which is dominated by guerrilla and paramilitary groups, the award citation said.
Its aim is to encourage women to redefine their position in society and to restore civil life in Colombia.
The Per Anger Prize, named after a Swedish diplomat who aided Raoul Wallenberg in helping Jews escape Nazi-occupied Budapest during World War II, was instituted in 2004 by the Swedish government to advance efforts promoting human rights and democracy.