The middle level, which is used by Madrid Metro Lines 6 and 10, is partially underground and has a dual-island platform with four tracks arranged to facilitate cross-platform transfers.

The original station had a simple construction and opened in June 1861, although the line initially only offered service to El Escorial near Madrid.

Due to a lack of space, maintenance facilities were built alongside the track between the station and the Puente de los Franceses.

On 16 July 1882, the first of the station's two passenger halls was inaugurated,[4] located parallel to the tracks and facing the Paseo de la Florida.

In order to solve this difficulty, on 26 December 1925, Madrid Metro opened a branch of its Line 2 between the Estación del Norte and Isabel II station (today Ópera),[5] allowing travelers to take the subway rather than climb the hill.

[4] In those years, the Estación del Norte became the second busiest railway station in Madrid after Atocha with service to northwestern Spain, Castile and León, and Portugal.

The station served as the terminus for a new direct line to Burgos that offered a shorter trip to Irun and the French border than the older route through Valladolid.

The same year, the so-called Túnel de la Risa ("Tunnel of Laughter") opened, connecting Atocha and Chamartín stations and allowing trains to pass underneath the city center.

Between 1985 and 1992, Atocha was closed for renovations, and trains from southern Spain and the Mediterranean coast were rerouted to Chamartín via the Túnel de la Risa.

On 30 January 1993, the last long-distance train departed the Estación del Norte, and it closed for an extensive renovation planned by engineer Javier Bustinduy.

The renovation coincided with the Pasillo Verde Ferroviario (Green Rail Corridor) project, which was intended to improve the Cercanías ring route around Madrid.

The project replaced a neglected surface rail line with a tunnel between the Estación del Norte and Delicias station.