The credit union was chartered in 2010 to serve members and employees of Unity, the Way of Holiness Christian Church in Charlotte and Clarkton. It had deposits of about $379,000 and served about 1,400 members.
Deposits are insured up to $250,000. The NCUA will issue checks to members with their deposits within one week.
Members of Shepherd's can call the regulator's Consumer Assistance Center hotline at 800-755-1030 with questions.
It's the fourth credit union liquidation so far this year.