Thomas was taken into custody and charged with failing to report child abuse or neglect.
Thomas is listed as the director of The Teaching Learning Center at Ocean View Baptist Church.
Parents received a letter on Friday saying that Thomas was no longer director and there would be an interim director put in place.
Mary Lynn Boggs, 46, a worker at the daycare was charged with three felony counts of Unlawful Neglect of a Child on Thursday.
Myrtle Beach police started investigating allegations two weeks ago that Boggs was holding children down under blankets during nap time.
Thomas has been released from the Myrtle Beach jail on a personal recognizance bond.