The 58-year-old actor, who has been a lifetime fan of the show since it premiered in 1963, took over the role in 2013, becoming the 12th actor to control the TARDIS.
He first appeared briefly during the 50th anniversary special in November 2013, before Matt Smith's Doctor regenerated in the Christmas special the following month.
Capaldi has starred in two seasons of Doctor Who so far and three Christmas specials. The 10th series of the show, his third as The Doctor, will premiere later this year.
He will be joined by newcomer Pearl Mackie, who has replaced Victoria star Jenna Coleman in the role of companion.
The news comes a year after Steven Moffat revealed he would be stepping down as showrunner and head writer this year.
Moffat, who joined the show in the first season in 2005, replaced Russell T Davies as showrunner in 2010 after Davies and then-Doctor David Tennant stepped down.
Chris Chibnall, best known for writing crime drama Broadchurch, will take over as head writer for the 11th season next year.
Capaldi visited New Zealand in 2015 to promote the show, where he spoke about his wish for Peter Jackson to direct an episode.
