On 20 December 1893, industrialist Adolf Guyer-Zeller applied for a concession to build a cogwheel railway from the station of the Wengernalp Railway (WAB) on Kleine Scheidegg to the summit of the Jungfrau, via a long tunnel through the Eiger and Mönch mountain. The Federal Council granted the concession on 21 December 1894. From the very start, Guyer-Zeller planned for the Jungfrau Railway to be driven by electricity and thus obtained the water rights to the two Lütschinen rivers. On 10 June 1896, he was granted the concession to build a power plant.

On 27 July 1896, ground was broken for the construction of the Jungfrau Railway. Despite the connection to the Wengernalp Railway, other systems were chosen: a different gauge (1,000 mm instead of 800 mm), another rack (Strub instead of Riggenbach) and three-phase current instead of alternating current as this promised increased power and reliability. Construction progress was slow and laborious. On 19 September 1898, the section in open terrain from Kleine Scheidegg station to the Eigergletscher (Eiger Glacier) station at the foot of the Eiger was put into service. The official opening of the Eigergletscher station was marked by a religious service held by Gottfried Strasser, the "“Glacier Priest”" from Grindelwald. Guyer-Zeller’s intention was to reach one additional station each year and open it as quickly as possible.

On 7 March 1899, ground was broken at Rostock station, which was operated only temporarily. The station facilities are now largely dismantled. Today, only a door that leads into the open serves as a reminder of this station. On 7 March 1899, workers at the head of the tunnel reached the intended site of the Eigerwand station. Adolf Guyer-Zeller, the driving force behind the Jungfrau Railway, died on 3 April of the same year. Guyer-Zeller's sons continued the construction, but it was 28 June 1903 before the Eigerwand station in the middle of the north face of the Eiger (2,865 m above sea level) could be officially opened. Passengers were subsequently able to enjoy a view towards Grindelwald from the terrace. Two years later, on 25 July 1905, it was possible to open the section to the stop at Eismeer, some 3,160 metres above sea level, providing guests with a stunning glacier view. The railway's temporary tourist centre was also housed in the Eismeer station. The original plans were changed as a result of finances becoming stretched as well as due to Adolf Guyer-Zeller’s death. Instead of planning a station below the Mönchsjoch and continuing the railway to the Jungfrau summit, the Jungfraujoch became the end of the line.

The history of the construction of the Jungfrau Railway is marked by blasting accidents, strikes and financial problems. It was not until 1912 that the section to the Jungfraujoch, 3,454 metres above sea level, was completed – nine years later than originally planned. It is noteworthy that the Eismeer to Jungfraujoch section first operated as an adhesion railway and then as a cogwheel system in the last section before the Jungfraujoch. Therefore, special locomotives for use with adhesion and cogwheel systems had to be acquired. It was not until 1951 that the entire railway was converted to a cogwheel system, thus simplifying operations. 

The Jungfrau Railway, more than 100 years after its launch, still runs today on the same stretch to the Eigergletscher station and through the 7.6 kilometre tunnel to Jungfraujoch. Otherwise, there is little reminder of the founding period. Modern rolling stock brings travellers in a considerably shorter time to the Jungfraujoch – Top of Europe, which has since become a world-famous destination. In 1912, the trip still took 1 ¼ hours, and now the travel time is only 25 minutes. On the Sphinx terrace, re-designed in 1996, guests can expect an unrivalled view across the high Alpine Aletsch region and the Swiss Plateau. The largest ice palace in the Alps offers an intensive insight into the interior of the glacier. The Snow Fun Park and the high-quality staging of «Alpine Sensation» – a journey through the history of the Jungfrau Railway construction – are additional attractions that make an excursion to the Jungfraujoch worthwhile. Four modern restaurants and two bars provide a wide range of cuisine.