Very Rev Dr Lorna Hood was honoured for "exceptional and long service to the Church of Scotland" and "promoting tolerance and understanding" through raising awareness of the 1995 Srebrenica massacre in Bosnia.
She said: "It has been a wonderful day shared with my husband Peter and our children, Laura and Michael."
Collecting her award the day after Ratko Mladic was found guilty of genocide and other atrocities during the 1990s Bosnian war, Dr Hood the occasion was "very poignant".
She added: "Important though Mladic is, he is but one man in a web of violence and slaughter that spread over Srebrenica and other towns and villages in the region.
"As yet those thousands who carried out his orders remain at large often living in the same communities and in positions of responsibility."
Dr Hood, who served as Moderator at the Church of Scotland's General Assembly between 2013 and 2014, established the Scottish board of the charity Remembering Srebrenica.
She dedicated the award to the Mothers of Srebrenica organisation and survivors of the killings who have spoken out against hate and intolerance.
Dr Hood first visited Srebrenica in 2013, when she visited the location of the massacre and met the mothers of some of the victims.
Click here to listen to Premier's Alex Williams speaking with Very Rev Dr Lorna Hood: