Operations on the route were suspended last year following floods that caused damage to some crucial parts of the track.
Central East Africa Railways (CEAR) communication officer, Chisomo Mwamadi, said their engineers have completed rehabilitation on the railway line and the first trip takes off on Saturday.
The Lower Shire valley comprises districts such as Nsanje, Chikhwawa, Nchalo among other districts.
The route is very crucial as it serves a majority of people who do business between the two districts, who were forced to find other means of transport in the absence of the trains.
The suspension of the train operations between Limbe and the lower shire resulted in an increase in road transport business for lorry operators.