Kelly is currently comms director at the Financial Services Authority (FSA) and will take up his new post at Network Rail in November.
He will report to Network Rail’s CEO Sir David Higgins, who took up the role in February after leading the Olympic Delivery Authority.
Kelly told PRWeek: ‘I’m going back to the world of transport and staying in an area I know best – the area of regulated companies.’
Kelly’s previous roles include director of comms at BAA, comms director at the Northern Ireland Office, official spokesman for former PM Tony Blair and a BBC journalist.
Kelly, who took over as Blair's head of comms from Alastair Campbell in 2001, joined the FSA in May 2010.