The works include the design and construction of a 306m wharf extension, seven berthing dolphins plus the supply and installation of wharf conveyor modules.
A Clough spokeswoman told MiningNews.net that the value of the contract was confidential.
The company said project engineering had started, while procurement and planning work was scheduled to start this month.
Construction is slated for May 2014 with completion by early 2015.
Clough CEO Kevin Gallagher said the contract represented a significant milestone for the company and gave it the opportunity to expand its mining presence.
"As the recognised market leader in near-shore marine project delivery for the Australian oil and gas sector, this is a great opportunity for BAM Clough to participate in Fortescue's growth journey for the first time and bring our full suite of design and construction services to the Australian mining and minerals sector," he said.
"We will draw on BAM Clough's extensive local and international resources and 50-year track record in local project delivery to ensure this important project is safely delivered to Fortescue's cost, schedule and quality requirements."
BAM Clough is a 50:50 joint venture between BAM International and Clough, established in 1964.
It has previously completed work on major jetty and near-shore projects in Australia and Papua New Guinea, with a particular focus on oil and gas developments.