After rail privatisation, Chiltern Railways took over the rail services in 1996 and developed the interurban service to Birmingham Snow Hill.
 In 2002, a service to Kidderminster was opened.
The line was restored to double track the same year, and Marylebone was expanded in 2006 with two extra platforms in Chiltern's Evergreen 2 project.
A new platform (platform 6) was inaugurated in May 2006, while Platform 5 and the shortened platform 4 opened in September.
Platforms 5 and 6 were built on the site of the goods sidings and a depot was opened near Wembley Stadium railway station.

In September 2007, the Office of Rail Regulation granted the Wrexham Shropshire & Marylebone Railway (WSMR) Company permission to operate services from Wrexham in North Wales via Shrewsbury, Telford and the West Midlands to Marylebone; they started in early 2008, restoring direct London services to Shropshire (Wrexham already being served by a Virgin Trains service to Euston), with five return trips per day on weekdays.
This was reduced to four trains a day in March 2009.
These services ceased in January 2011 after passenger numbers reduced; the closure was blamed on the Great Recession.

In December 2008, it was proposed to restart direct services between Aberystwyth in mid-Wales and London, which last ran in 1991, with Marylebone as the London terminus.
Arriva Trains Wales announced a consultation for two services a day, following the route of the WSMR connecting with the Cambrian line at Shrewsbury.
This idea was abandoned following objections by Wrexham & Shropshire.

In 2011, Chiltern Railways took over the Oxford to Bicester Town route from First Great Western, in preparation for the opening of a link from the Chiltern Main Line to the Varsity Line (on which Bicester Town station is located), which would see twice-hourly services from Marylebone to Oxford.
Construction was expected to start in 2011 but was delayed until the following year after bats were found roosting in one of the tunnels on the Varsity line.
Services to Oxford Parkway started in October 2015 and services to Oxford began in December 2016.
In 2018, a survey found that commuters from Oxford preferred the Chiltern route to Marylebone over the Great Western route to Paddington via Reading.

In 2017, Network Rail proposed an upgrade of Marylebone with 1,000 extra seats on trains approaching the station.
These improvements are planned to be complete by 2024.
Beyond this, improvements to Old Oak Common station are planned to relieve congestion at Marylebone.

In a study by Network Rail it was said that any expansion of the station could cost up to £700 million with Old Oak Common a more feasible alternative for capacity increase.
After rail privatisation, Chiltern Railways took over the rail services in 1996 and developed the interurban service to Birmingham Snow Hill.  In 2002, a service to Kidderminster was opened. The line was restored to double track the same year, and Marylebone was expanded in 2006 with two extra platforms in Chiltern's Evergreen 2 project. A new platform (platform 6) was inaugurated in May 2006, while Platform 5 and the shortened platform 4 opened in September. Platforms 5 and 6 were built on the site of the goods sidings and a depot was opened near Wembley Stadium railway station.
In September 2007, the Office of Rail Regulation granted the Wrexham Shropshire & Marylebone Railway (WSMR) Company permission to operate services from Wrexham in North Wales via Shrewsbury, Telford and the West Midlands to Marylebone; they started in early 2008, restoring direct London services to Shropshire (Wrexham already being served by a Virgin Trains service to Euston), with five return trips per day on weekdays. This was reduced to four trains a day in March 2009. These services ceased in January 2011 after passenger numbers reduced; the closure was blamed on the Great Recession.
In December 2008, it was proposed to restart direct services between Aberystwyth in mid-Wales and London, which last ran in 1991, with Marylebone as the London terminus. Arriva Trains Wales announced a consultation for two services a day, following the route of the WSMR connecting with the Cambrian line at Shrewsbury. This idea was abandoned following objections by Wrexham & Shropshire.
In 2011, Chiltern Railways took over the Oxford to Bicester Town route from First Great Western, in preparation for the opening of a link from the Chiltern Main Line to the Varsity Line (on which Bicester Town station is located), which would see twice-hourly services from Marylebone to Oxford. Construction was expected to start in 2011 but was delayed until the following year after bats were found roosting in one of the tunnels on the Varsity line. Services to Oxford Parkway started in October 2015 and services to Oxford began in December 2016. In 2018, a survey found that commuters from Oxford preferred the Chiltern route to Marylebone over the Great Western route to Paddington via Reading.
In 2017, Network Rail proposed an upgrade of Marylebone with 1,000 extra seats on trains approaching the station. These improvements are planned to be complete by 2024. Beyond this, improvements to Old Oak Common station are planned to relieve congestion at Marylebone.
In a study by Network Rail it was said that any expansion of the station could cost up to £700 million with Old Oak Common a more feasible alternative for capacity increase.
Marylebone station