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.
A train guard has pleaded not guilty to causing the death of a 16-year-old girl at a Liverpool train station.
Christopher McGee, from Edenhurst Avenue in Egremont, is charged with the manslaughter of Georgia Varley.
The 45-year-old is also accused of failing to take reasonable care for the health and safety of others.