Rasema Handanovic, 39, was sentenced to five and a half years for the killings of six Bosnian Croats during an attack on the southern village of Trusina in April 1993.
The judge, Jasmina Kosovic, said Handanovic had been the victim of a wartime rape and had lost several family members in the conflict.
"The court has taken into account that Handanovic admitted the crimes, was willing to provide all information and evidence related to the attack and the fact that she expressed remorse to the relatives of the victims," Kosovic said.
Under a plea bargain she admitted the crimes and agreed to testify against six other members of the Zulfikar special unit of the Bosnian army that carried out the attack.
A total of 18 Croat civilians and four prisoners of war were killed in the attack, in which Handanovic was accused of taking part in a firing squad-style execution.
Handanovic, a naturalised US citizen, was extradited to Bosnia from the US, where she had been living in a suburb of Portland, Oregon.
The only other woman to have been convicted of war crimes during the Bosnian war was Biljana Plavsic, the former Bosnian Serb president, who was found guilty of persecution and crimes against humanity by the Hague-based war crimes tribunal for the former Yugoslavia.
Plavsic was sentenced in 2003 to 11 years in jail and was released after serving two-thirds of her term.