Most Rev Benjamin Kwashi was at home at the time of the attack along with 60 orphans in his care.
According to religious freedom charity Release International, one of his neighbours was killed while they seized nine cows.
Writing on his Facebook page, the Archbishop Benjamin said: "Adamu Dung was shot through the head because he flashed his light when he heard footsteps of cattle being rustled.
"The cows were mine. Adamu was killed. He is no threat. He is an ordinary citizen struggling with life and doing every honest job to make ends meet.
'We are not safe in [our] homes. I am raising an alarm - if the government will listen. Lord in your mercy."
Archbishop Kwashi has called repeatedly for the government to step up security to protect Christians under attack in the north.
Backing his call, Release CEO Paul Robinson said: "These murderous raids beg important questions. Why is the military apparently powerless to stop the slaughter of unarmed farmers? Who is arming and training these Fulani militants? And whose agenda does this killing of mainly Christian communities serve?
"It all points to a strategy to drive out Christians from the north of Nigeria.
"The government of Nigeria must protect its vulnerable Christian communities in the north - and its Anglican archbishop."
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