Abellio was founded by NS as NedRailways in 2002 to take advantage of the liberalisation of the European transport sector. In 2003, a 25 year franchise to operate Merseyrail was won in a joint venture with Serco. Northern Rail followed in 2004 - won by the same joint venture. The Northern Rail franchise ended in 2016.

In 2009, NedRailways was rebranded to Abellio after the purchase of Abellio Deutschland. This acquisition also meant the expansion from an owning group with two UK rail franchises to a European public transport company. In the same year, first steps into the London bus market were made by buying London Bus from National Express.

The first solo UK rail franchise was won in 2012 by winning Abellio Greater Anglia.

Furthermore, 5 rail bids in Germany turned out successfully and Qbuzz in The Netherlands was acquired.

In October 2014, Abellio was awarded the contract to operate ScotRail - Scotland's National Railway. The franchise started on 1 April 2015.

In August 2016, it was announced that Abellio was awarded the next East Anglia franchise which will run up to 2025. The new franchise 'Greater Anglia' commenced on 16 October 2016.

In August 2017, West Midlands Trains Ltd was announced as the winning bidder to run the next West Midlands rail franchise. The franchise, running under two seperate brands London Northwestern Railway and West Midlands Railway, commenced on 10 December 2017. WMT is a joint venture, owned by Abellio and its partners for the bid, Mitsui and East Japan Railway Company (JR East). In 2017, Qbuzz was sold to Busitalia, meaning that Abellio now focuses on UK and Germany.

In December 2017, Abellio Deutschland became the sole shareholder of WestfalenBahn, adding it to the German portfolio.