His departure comes in the middle of a criminal investigation into alleged improper euthanasia practices at the shelter.
Officials would only confirm his retirement.
This comes a little more than six weeks after McGee and his assistant, Shannon Barlow, were placed on leave while the investigation into animal control's euthanasia practices took place.
Citizens have been calling for McGee's firing or resignation since the controversy first erupted April 11.
Amarillo Police and the Randall County DA's office wrapped-up their investigations into accusations of animal cruelty weeks ago.
However, a grand jury has yet to make a decision on any possible charges.
Animal activist Shea White, who has been calling on McGee's resignation, says this is more than an emotional issue.
The Randall County DA says when the grand jury does make its decision. Not everyone may be happy with the outcome.
The grand jury's decision will come in two weeks.
White says Barlow needs to be the next to go.
She says there is very little confidence in the previous leadership at animal control.
Scott McDonald remains as the interim director of animal control.
He has made several policy changes since taking over including the addition of a lost-pets website to help reunite pets with their owners.