Uganda transferred $65 million to its western neighbor on September 1, according to minutes of a cabinet meeting released at the weekend.
The sum is the first of five annual payments Kinshasa was awarded in damages and interest by the International Court of Justice (ICJ) in February, Justice Minister Rose Mutombo told ministers on Friday.
The decision was issued after a years-long legal battle mounted by Kinshasa for Uganda's invasion in the 1998-2003 conflict.
At its height, the conflict drew in nine African countries, with Uganda and Rwanda backing rebel forces against the Congolese government as they jostled for control of mineral-rich Ituri province.
The ICJ said that of the $325 million, $225 million was for loss of life, $40 million for property damage and $60 million for damage to natural resources.
DR Congo had demanded $11 billion.
The money is being held in a Congolese bank in a provisional justice ministry account, the cabinet was told.
It cannot be used until a special compensation fund for victims becomes operational.
Kampala lashed the ruling as unjust and incorrect, noting it was delivered as relations between the two countries have been improving.
Uganda and the Democratic Republic of Congo launched a joint operation last November against the Allied Democratic Forces (ADF), a bloody militia that the Islamic State group says is its central African affiliate.