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
Arriva confirms strike action twill go ahead. There'll be no Arriva bus services in Merseyside, Manchester, Lancashire or Cheshire
The North's historic textile mills are disappearing fast despite massive public support against demolition, Historic England said today.
Cloudier skies, milder air, spells of rain and stronger winds. A milder but more unsettled story over the coming days