The first freight train on the standard gauge railway left Mombasa for Nairobi on Monday.
The train, hauling 52 wagons, left Port Reitz Freight station at 5.30am and was expected at Nairobi's Inland Container Depot at 2.20pm.
The train ferried a total of 20 containers of maize and 32 Through Bill of Lading containers. A freight train only carries goods.
The freight services started after President Uhuru Kenyatta commissioned the upgraded Inland Container Depot (ICD) in Embakasi last December.
Standard Gauge Railway (SGR) Freight coordinator Hamisi Disi said that the cargo would be offloaded at the ICD in Embakasi for clearance before owners collect them.
"This is the first freight train to operate on the new SGR line this year," Disi said.
The ICD is now under the management of the Kenya Ports Authority (KPA) which is overseeing its operations.
The port was constructed by the China Communications Construction Company (CCCC) before it was handed over to KPA.
It has a centre housing representatives from Rwanda, Uganda, Burundi and the Kenya Revenue Authorities. The officials are responsible for, among other things, clearing goods that leave the Port of Mombasa before being cleared.