The company promptly commenced the redoubling of the Chiltern Main Line under the Evergreen initiative and ordered the Class 168 Clubman diesel multiple units (DMUs) to supplement its ex-British Rail fleet.

Following the awarding of a 20-year franchise to Chiltern Railways in August 2000, Evergreen phase 2 works begun to raise line speeds around Beaconsfield, built two new platforms at its London Marylebone terminus.

In January 2010, a £250 million upgrade package was agreed for Evergreen phase 3, remodelling the line and permitting 100 mph operations, thus greatly reducing journey times.

However, the team recognised that they lacked the resources to successfully pursue a bid, thus they secured the backing of the infrastructure investment group John Laing and the venture capital specialist 3i.

[2][6] In March 2000, the Shadow Strategic Rail Authority announced that both M40 Trains and the British transport group Go-Ahead had been shortlisted to bid for the next Chiltern franchise.

[13] During December 2004, Chiltern Railways took over operation of passenger services on the Leamington Spa to Stratford-upon-Avon branch line from First Great Western Link.

In 1996, the British retailer Tesco sought to build a supermarket near Gerrards Cross railway station; despite the local council's initial objection to the scheme, it was approved by the Deputy Prime Minister John Prescott in July 1998.

[16] Due to a lack of available space, Tesco started building a tunnel over the active railway line to provide suitable land for the development.

On 30 June 2005, the partially-constructed tunnel collapsed; nobody was injured, but a complete closure of the line was enacted for over six weeks before being permitted to reopen on 20 August 2005.

[16] Tesco paid an estimated £200 million of compensation to both Chiltern Railways and Network Rail for the disruption; the retailer also pledged to fund a media campaign to win back passengers lost by the route's unplanned closure.

[31] In 2021, following the COVID-19 emergency measures, Chiltern was awarded a new direct contract by the DfT, replacing its franchise agreement, with a core term until 1 April 2025 and expiring on 12 December 2027.

The route links the major cities of London and Birmingham (Marylebone and Snow Hill stations respectively), passing through the towns of High Wycombe, Banbury, Royal Leamington Spa, Warwick and Solihull.

As of May 2023, a simplified description of the routes served off-peak Monday to Friday are as follows:[38][41] Chiltern Railways operates two parliamentary train services:[38] On certain Bank Holiday Mondays, services are extended from Aylesbury to the Buckinghamshire Railway Heritage Centre facilities at Quainton Road, a short way north of Aylesbury Vale Parkway.

Until January 2022, Chiltern offered a premium economy "Business Zone" carriage on their Class 68 loco-hauled services between Birmingham or Oxford and London.

During 1998, its poor performance figures in criteria such as reliability, punctuality, and customer approval has led to financial penalties being incurred by the company, some of which was in the form of refunds to its passengers.

[2] By the mid-2010s, Chiltern was considered one of the best railway operators in Britain, with Public Performance Measure (PPM) regularly over 90%,[49] until the introduction of changes in November 2015,[50] and infrastructure issues saw punctuality fall to 86% in December 2015.

Performance figures published by Network Rail rate Chiltern Railways sixth in train operating companies in the UK at 89.4% (PPM – period 9) and 94.3% (MAA) for the year to 12 December 2015.

[58][59] Phase 1 of the project, now complete, involved upgrading the Marylebone – Birmingham Chiltern Main Line to permit 100 mph (160 km/h) running on an additional 50 miles (80 km) of route.

Accelerated services were initially planned to start in May 2011, but there were delays and it was not until 5 September 2011 that Chiltern was able to introduce a new timetable to take advantage of the improvements.

Chiltern Railways former chairman Adrian Shooter stated: "This is the biggest passenger rail project for several generations not to call on the taxpayer for support.

This deal demonstrates that real improvements to rail services can be paid for without public subsidy by attracting people out of their cars and on to trains."

[58] During October 2012, the Secretary of State for Transport granted permission for work to begin on Phase 2 of the Evergreen 3 project, with services between London Marylebone and Oxford.

Network Rail provided the capital for the upgrade and will recover this through a facility charge over the subsequent 30 years, initially payable by Chiltern until its franchise expires, and then by the next franchisee.

[58][65][66] Oxfordshire County Council supported the scheme, but required convincing of the benefits of the new Oxford Parkway station at Water Eaton, which is in the Green Belt.

[87] Between 2003 and 2005, all 39 Class 165s were overhauled by Bombardier at Ilford EMU Depot; during this work, air conditioning units were installed throughout the fleet, while the hopper opening windows were removed; a first-class seating area was also implemented.

[97] Starting in December 2010, Chiltern began operating two peak-hour loco-hauled services consisting of a Class 67 diesel locomotive hauling a rake of Mark 3 coaches and a Driving Van Trailer.

[100] In 2012, the DB-Regio-owned Mark 3s used on the peak-hour Banbury service were given a light overhaul at LNWR, Bristol, and the Virgin-liveried examples repainted into British Rail blue/grey.

[104] During 2017, Chiltern Railways entered into an agreement with Artemis Intelligent Power and the Rail Safety and Standards Board to provide one of its redundant DVTs as a donor vehicle for conversion into a new type of diesel locomotive.

[105] In July 2021, Chiltern Railways converted a single Class 168 unit (168329) into a Battery Hybrid train, referred to as "HybridFlex"; during February 2022, it was first run on services between London and Aylesbury.

[106][107] The company promoted the HybridFlex as increasing acceleration while reducing fuel consumption, vibration, and noise emissions, along with lessening the environmental impact of rail travel.