Gee had been under fire for his handling of a case in which a BART officer shot and killed an unarmed passenger. The shooting of Oscar Grant was caught on video and several officers and board of directors members called for Gee's resignation.
The 64-year old police chief says he is voluntarily stepping down.
In the memo he states, "My 36 1/2 years of service with the nation's finest transit police department have been a privilege. I hope to remain on the job until a new chief of police is appointed."
His resignation is effective December 30.