The court ruled that general Jerome Kakwavu was guilty of committing serious violations including the repeated rapes of two females, two murders and acts of torture on two other people.
He had also failed to take "necessary measures" to prevent and stop "war crimes by murder ... Committed by men under his command."
The court issued a tougher sentence than sought by the public prosecutor, who had demanded eight years.
Kakwavu is the highest ranking national army officer to be convicted for war crimes since the start of the first Congo War in 1996.
He became an army general by presidential decree when his rebel group was integrated into the military in December 2004. He was arrested shortly afterwards.
Violence has plagued eastern Democratic Republic of Congo (DRC) for the past decades, as rival militia seek control over a region rich in minerals, diamonds and timber.