The main line between the port of Matarani, Arequipa, Cusco and Puno on Lake Titicaca was formerly known as the Ferrocarril del Sur (Peru Southern Railway), and was for a time owned and operated by the ENAFER state company.

From Cusco, PeruRail provides passenger services on the 3 ft (914 mm) gauge Ferrocarril Santa Ana to Aguas Calientes, delivering tourists for Machu Picchu.

The line between Cusco and Machu Picchu - Ferrocarril Santa Ana - is a 3 ft (914 mm) narrow gauge line, which boasts a series of five switchbacks called locally 'El Zig-Zag', which enable the train to climb up the steep incline out of Cusco, before it can begin its descent to the Sacred Valley of the Incas and then continue down to Machu Picchu.

From Poroy, the narrow-gauge line goes northwest to Ollantaytambo, where the branch from Urubamba joins, then on to Machu Picchu station in Aguas Calientes.

Tracks formerly continued into the jungle, but they were destroyed by recent flooding.The 4 ft 8+1⁄2 in (1,435 mm) standard gauge network, formerly Ferrocarril del Sur, starts at Matarani port, goes through Arequipa and enters Puno Region, where the line splits in two at Juliaca.

PeruRail's own lower category Pullman service with dining and observation/bar car resembling to Titicaca Train (see below) was introduced 2017 with the name Sacred Valley.

Although not advertised, PeruRail also offers local trains equipped with wooden seats, which are available only to Peruvian nationals for a fraction of the price charged to tourists.

The main products transported by PeruRail are copper concentrates, fuel, wheat (for Peruvian and Bolivian consumption), coal, cement, soya flour from Bolivia, coffee, beer and non-alcoholic beverages.