The hearing for Nathan Sutherland Tuesday only lasted a few minutes, with him identifying himself and stating his date of birth. His next court appearance was set for March 19.
Authorities say Sutherland, 36, was working at a licensed practical nurse at Hacienda Healthcare in Phoenix when he raped the 29-year-old victim, who has been in long-term care since age 3 after suffering a near-drowning. He has been held on $US500,000 ($699,075) bail since last month.
Authorities say Sutherland raped the 29-year-old victim at Hacienda HealthCare. Investigators collected DNA samples from all male employees of the facility.
Dave Gregan, Mr Sutherland's lawyer, told reporters outside the court that his client "is entitled to due process of the law".
Employees at the facility at the time said they didn't know the victim was pregnant.
Sutherland's attorney has argued there was no direct evidence linking Sutherland to the rape.
Initially described as comatose by police, the woman's family later said in a statement that she is able to respond to sound and has some ability to move her body.
Mr Ducey, in a letter, also called for the Attorney-General to seek civil penalties against Hacienda and a reorganisation, "to ensure that nothing like this ever happens again".
The facility said in a written statement that Sutherland was sacked as soon as administrators learned of his arrest, and that he had undergone extensive background checks before being hired.
FILE PHOTO: Nurse Nathan Sutherland is shown in this booking photo in Phoenix, Arizona, U.S., provided January 23, 2019.
The boy, who is healthy, has been staying with family members who are part of the Native-American Apache tribe.
Hacienda has since retained an Indiana-based company, Benchmark Human Services, to oversee operations at the nursing facility after Arizona regulators ordered the site placed under independent management. But Ducey said the company has since said it can not afford the cost of such outside management.