Tom Ellis was born in Bangor, Gwynedd, North Wales. His father, sister and uncle are all church ministers, with his uncle Robert Ellis being Principal of Regent's Park College, Oxford, which his father Chris also attended. Ellis attended High Storrs School in Sheffield during his education and was a French Horn player in the City of Sheffield Youth Orchestra.
Ellis was married to actress Tamzin Outhwaite from 2006 to 2014. On 25 June 2008, she gave birth to their first daughter, Florence Elsie Ellis. He has another daughter, Nora Ellis, from a previous relationship. On 20 December 2008, the pair appeared on ITV gameshow All Star Mr & Mrs Christmas Special. On 19 March 2012, Ellis announced via his Twitter account that Outhwaite was pregnant with their second child together; their daughter Marnie Mae Ellis was born 2 August 2012.
On 29 August 2013, Ellis and Outhwaite announced their separation. Their spokesperson stated that the couple had separated and the following month, Outhwaite filed for divorce, citing Ellis' infidelity as the grounds for dissolution of the marriage.
Other notable roles include Justyn in Channel 4's No Angels and Thomas Milligan in the series three finale of British science-fiction television programme Doctor Who. In 2013, he was cast as Victor Frankenstein ("a brilliant doctor who's trying to find a way to bring his late daughter, Anna, back to life") in the ABC pilot series Gothica, a modern-day supernatural drama. In February 2015 it was announced that Ellis was cast as Lucifer Morningstar in the Fox Television drama Lucifer, based on the comic with the same name. In July and August 2009, Ellis starred in ITV comedy drama Monday Monday with Fay Ripley. Ellis was the star of the USA network series Rush, playing a Hollywood physician.