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
Jose Mourinho's impending appointment as Manchester United boss could be being held up by Chelsea still owning the trademark to his name.
From Thursday, "legal highs" are to be legal no more, with the Psychoactive Substances Act coming into force. But what does it all mean?
10,000 children a year could be at ‘terrible risk’ because they receive no active police response when they go missing