At the outbreak of the 12-year war in 1993, Barankitse -- a Tutsi -- was forced to watch the execution of 72 of her Hutu neighbors.
That horrific incident inspired her to start a mission at the Catholic diocese where she worked. Caring for children and refugees, she created an environment where young Hutus and Tutsis alike could seek refuge.
Her heroic efforts have now been acknowledged by a $1m humanitarian prize.
Barankitse, now 59, was presented the Aurora Prize for Awakening Humanity
for her extraordinary efforts in caring for orphans and refugees by Hollywood actor George Clooney.
"Marguerite Barankitse serves as a reminder of the impact that one person can have even when encountering seemingly insurmountable persecution and injustice," said Clooney, a co-chair of the Aurora Prize selection committee, at the award ceremony in Yerevan, Armenia, last month.
Launched this year, the Aurora Prize recognizes exceptional individuals who have preserved human life in the face of adversity, risking freedom, reputations, livelihoods, or even their lives.
Accepting the award Barankitse, said: "Our values are human values.
"When you have compassion, dignity and love, then nothing can scare you, nothing can stop you. No one can stop love -- not armies, not hate, not persecution, not famine, nothing."
"This prize is consolation for the whole of Burundi's people."
Donates $1m to Burundi's young
Barankitse's humanitarian efforts didn't stop when the war ended.
In 2008, three years after the conflict, she opened a hospital in Burundi, which has since treated more than 80,000 patients.
Currently in Rwanda, she is now helping Burundian refugees in camps along the border.
Barankitse says she will use the $1 million grant -- for her to donate to a charity or organization that has inspired her -- to send children in this region to school, and to help young people who suffered injuries during the civil war.
Barankitse was also personally awarded $100,000.