Georgia Varley died in James Street underground station last October.
It is thought she got off her Wirral Line train a stop too early and slipped between the carriage and the platform.
Mr McGee is accused of failing to carry out a final safety check before giving the signal for the train to depart.
He will face trial at Liverpool Crown Court in November.
More top news
Two boys from Oldham have been sentenced after an horrific attack which left a teenager with brain damage.
A video showing the moment a carriage on the Smiler rollercoaster at Alton Towers crashed into an empty car has been shown in court.
A mixed week ahead