The Ordall Chord project will link Manchester Victoria and Manchester Piccadilly stations by rail for the first time.
It is the largest part of a £200m programme of work won by the Bam Nuttall/Skanska JV in 2013 to improve the rail links across Manchester.
Amey will join the team to assist with the construction of the Ordsall Chord, with Siemens leading the signalling, power and communications work on the line.
The Ordsall Chord is a central part of Network Rail’s £600m Northern Hub rail improvement programme, which was given the green light by transport secretary Patrick McLoughlin in March 2015.
However, a legal challenge from former Institution of Civil Engineers president Mark Whitby on the grounds the project would “substantially harm” the city’s heritage threatened to derail the programme.
Last week, Mr Whitby’s attempt to stop construction on the site was rejected by the Court of Appeal.
Work is now expected to be completed by December 2017.
Network Rail’s manager of the alliance Mike Heywood said: “Within this alliance of organisations, we have a wide range of skills and experience to make this vital new stretch of railway a reality and deliver the service all rail passengers deserve.”
Amey account director James McDermott said: “This alliance brings together the best experience and expertise in the industry and we’re looking forward to working in partnership to deliver significant improvements to connectivity in the north. “