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
Although high to very high counts are expected in the driest, warmest weather, counts will generally be tailing off this coming week
A collection of dramatic pictures sent in by our viewers of the storms that crossed our region last night.
Fine evening on Saturday. Wet again for all parts at some point on Sunday. Cooler and more changeable for the new week