For most of its journey, the train also runs along the World Heritage Site known as the Rhaetian Railway in the Albula / Bernina Landscapes.

It takes the form of an enhanced regional service between Tirano and Chur: panoramic coaches with enlarged windows and multi-lingual (English, Italian and German) audio guide on board.

It is not an "express" in the sense of being a high-speed train; passengers must make a seat reservation either directly when they purchase Bernina Express tickets, or pay a small supplement on top of their regional train tickets.

The train leaves Pontresina and ascends progressively through the valley to the Bernina Pass over the Morteratsch station (1,896 m [6,220 ft]), where the glacier and the highest summit of the Eastern Alps, Piz Bernina (4,093 m [13,428 ft]) are visible.

During the summer, the Bernina Express comprises a special separate train that travels from Chur to Pontresina with very few stops.

In Pontresina, the locomotive is changed (because of the Bernina line's different electricity current) and the train continues with few stops to Tirano.

During autumn, winter and spring, the Bernina Express comprises several cars that are attached to regional services.