The track layout through and around the station was remodelled again in 1988 as part of the resignalling scheme that was carried out prior to the electrification of the ECML shortly afterwards. This resulted in several bay platforms (mainly on the eastern side) being taken out of service and the track to them removed. At the same time a new signalling centre (York IECC) was commissioned on the western side of the station to control the new layout and also take over the function of several other signal boxes on the main line.
The IECC here now supervises the main line from Temple Hirst (near Doncaster) through to Northallerton, along with sections of the various routes branching from it. It has also (since 2001–2) taken over responsibility for the control area of the former power box at Leeds and thus signals trains as far away as Gargrave and Morley.
In 2006–7, in order to improve facilities for bus, taxi and car users as well as pedestrians and cyclists, the approaches to the station were reorganised.
The former motive power depot and goods station now house the National Railway Museum.