The travel operator had bid for the nine-year contract to run train services in the East of England between Liverpool Street and Norwich, but it was awarded to Abellio which currently runs the service.
Abellio, a subsidiary of state-owned Nederlandse Spoorwegen, will run he service from October. It has pledged to deliver faster, more frequent journeys and a £1.4bn investment in rail services.
It planned to cut journey times by 10% on average across the region, with a new 90-minute service between Norwich and London.
Abellio also agreed a £1bn contract with Canadian manufacturer Bombardier.
“We are naturally disappointed because we delivered a disciplined bid that balanced significant customer improvement with excellent value to taxpayers and a fair return for shareholders,” said National Express in a statement today.