The city sits on one of the Azerbaijani primary rail lines running East-West connecting the capital, Baku, with the rest of the country. The Kars–Tbilisi–Baku railway will run along the line through the city. The railway provides both human transportation and transport of goods and commodities such as oil and gravel.
Ağstafa's Central Railway Station is the terminus for national and international rail links to the city. The Kars–Tbilisi–Baku railway, which will directly connect Turkey, Georgia and Azerbaijan, began to be constructed in 2007 and is scheduled for completion in 2015. The completed branch will connect the city with Tbilisi in Georgia, and from there trains will continue to Akhalkalaki, and Kars in Turkey.