The agency won the account in a four-way competitive pitch, replacing incumbent Atomic PR, which declined to re-pitch.
Flagship is to provide media relations, social media and content creation under the retained brief.
The agency is to help launch a manifesto for the rail industry. This includes identifying five key things the industry needs to do to be successful in the future.
In addition, there are plans to launch an integrated marketing campaign for the global rail industry. SilverRail operates from offices in London, Boston, Brisbane, Stockholm and Norrköping, employing around 200 people.
It comes as SilverRail looks to enter its "second phase" as a business, having reached the first phase of getting its technology ready.
Lisa Enns, marketing director at SilverRail, said "The next five years promise to be a revolutionary time for the rail industry, and we look forward to taking the ride with Flagship."
Sophy Norris, director of Flagship Consulting’s South West office in Exeter, said: "SilverRail is at the helm of a rail revolution. Flagship’s aim is to support and promote SilverRail as it connects global rail carriers with the worldwide ecosystem of travel distributors and managers. We cannot wait to begin communicating some of the campaigns that we have been planning with SilverRail’s team."