Matthews was educated at Esher Grammar School and worked as a freelance writer and journalist. He has written over 170 books on history, ghosts, cryptozoology, UFOs, paranormal activity, guides to the UK and children's stories. Matthews is the editorial director and a shareholder of Bretwalda Books.
Matthews has also run an online course about the paranormal for the International Metaphysical University, on whose website he was described as a 'Professor' until mid-January 2012.
He served as a councillor for St Mark's ward in Surbiton in Kingston upon Thames, and in the General Election of 1997 he stood in the safe Labour seat of Bootle.
Matthews was selected as a Conservative candidate for the 2009 European Parliament election and was placed third on the Conservative party list for the East Midlands. He was not elected.
On 12 October 2011 MEP for the East Midlands region Roger Helmer, announced that he would resign from the European Parliament at the end of the year. Helmer expected to be replaced by Matthews who had been next on the Conservative party list in the East Midlands.
However, after there was uncertainty whether the Conservative Party would approve Matthews as the new MEP, Helmer announced he would delay standing down until the position was clarified and Matthews confirmed as his successor. The Tory party was reported to be looking into golliwog dolls featuring on the front cover of a book on political correctness published by Bretwalda Books. It was later revealed that Rupert was not personally involved in publishing the book. In March 2012 Helmer defected to UKIP and remained a MEP; he was re-elected in 2014.
For the 2014 European Parliament election Matthews was again placed third on the Conservative party list for the East Midlands and, again, missed being elected.
In 2014, Matthews took up a position as National Campaigns Director at Better Off Out. He led Better Off Out's campaign for Britain to Leave the European Union, liaising with the official campaign (Vote Leave) as well as with Leave.EU and Grassroots Out. During this time Matthews supervised the production of leaflets, posters and other campaign materials as well as organising their distribution to the public in the run up to the United Kingdom European Union membership referendum, 2016.
He finally became a MEP for the East Midlands on 29 June 2017, replacing Andrew Lewer.
Matthews has been described as "a sceptic over the EU, but on precious little else". Reportedly he thinks the Lisbon Treaty could enable the European Commission to invade Britain should the country ever attempt to leave the European Union, or to request a German panzer (tank) division be sent to London if the situation should warrant it.