The firm released a new schedule for the trains that shuttle between the two counties.
Afristar will now have trains leaving Nairobi and Mombasa at the same time in the morning and two other trains leaving in the afternoon.
All is set for the resumption of a second Nairobi-Mombasa passenger train, with the first locomotive expected to leave the capital city on October 1 at 2.15pm.
In a notice, Madaraka Express operator Afristar said standard gauge railway (SGR) passenger train services will resume following the lifting of partial transport restrictions in Nairobi and Mombasa by President Uhuru Kenyatta.