The agreement is with Ports e Caminhos de Ferro de Mocambique, otherwise known as CFM.
The Sena Line starts about 3km from the Minas Moatize coking coal mine in Tete province and proceeds 580km (362 miles) to the port of Beira.
The company plans to use the rail capacity to start coking coal exports this year.
Beacon Hill chairman Justin Farr-Jones called the agreement an important step in its plan to start exports this year.
The Sena Line is nearing the completion of a $60 million upgrade program that will lift its capacity to 6.5 million tonnes per annum.
Minas Moatize will become the third major coal exporter to use the line, sharing capacity with Rio Tinto and Vale.
The company will initially operate two train sets, each consisting of two locomotives with 42 wagons. Each of those wagons will have up to a 63t capacity.
