Rogers joined EMR in January 2020. He guided the business through multiple lockdowns, retirement of the high-speed trains, refurbishment of all fleets and the introduction of the Aurora trains, said Transport UK.
He also led EMR in responding to the fatal train crash near Bedford on 19 June.
Dominic Booth, Transport UK CEO, said: “He has been instrumental in delivering exceptional service to our customers and has embodied the Transport UK delivery-first mentality.
“In recent weeks, Will has also given his all in responding to the tragic incident at Bedford South. I would like to thank Will for all his efforts and wish him the best in the future.”
Rogers said: “I am sad to say goodbye to a business and to colleagues who have meant so much to me.
“I have been incredibly fortunate to work alongside such talented, committed and caring people, and I will always be grateful for the experiences, friendships and memories we’ve shared.”