He takes over from Frédéric Delorme, who joined French railway company SNCF as head of security in January.
McNaughton joins Systra from Tidal Lagoon Power, where he was director of engineering and construction.
His appointment will see him working with Balfour Beatty again, this time as part of a joint bid team chasing civils contracts for HS2.
Systra, in joint venture with Mott MacDonald, is working as the design partner for the Balfour Beatty/Vinci HS2 bid team.
Guillaume Pepy, chairman of the executive board of SNCF, “The appointment marks a new chapter in Systra’s history.
“By including a British national in the senior management team, Systra’s shareholders have confirmed their commitment to the group’s international expansion.”