In addition to the televised episodes of Doctor Who starring Patrick Troughton, the Second Doctor has appeared in a number of spin-off media.

Audio dramas

• Fear of the Daleks (an adventure related by the character Zoe) (2007)
• Helicon Prime (an adventure related by the character Jamie) (2007)
• The Great Space Elevator (an adventure related by the character Victoria) (2008)
• Resistance (an adventure related by the character Polly) (2009)
• The Glorious Revolution (an adventure related by the character Jamie) (2009)
• The Three Companions (an adventure related by the character Polly)
• The Emperor of Eternity (an adventure related by the characters Jamie & Victoria) (2010)
• Echoes of Grey (an adventure related by the character Zoe) (2010)
• Prison in Space (an adventure related by the characters Jamie & Zoe) (2010)
• The Forbidden Time (an adventure related by the characters Polly & Jamie) (2011)
• Tales from the Vault (a short adventure related by the character Zoe) (2011)
• The Memory Cheats (an adventure related by the character Zoe) (2011)
• The Rosemariners (an adventure related by the characters Jamie & Zoe) (2012)
• The Selachian Gambit (an adventure related by the characters Polly & Jamie) (2012)
• The Jigsaw War (an adventure related by the character Jamie) (2012)
• The Uncertainty Principle (an adventure related by the character Zoe) (2012)
• Destiny of the Doctor: Shadow of Death (an adventure related by the character Jamie) (2013)
• The Light at the End (portrayed by Frazer Hines) (2013)
• House of Cards (an adventure related by the characters Polly & Jamie) (2013)
• The Apocalypse Mirror (an adventure related by the characters Jamie & Zoe) (2013)
• The Queen of Time (an adventure related by the characters Jamie & Zoe) (2013)
• Lords of the Red Planet (an adventure related by the characters Jamie & Zoe) (2013)
• The Dying Light (an adventure related by the characters Jamie & Zoe) (2013)
• Second Chances (an adventure related by the character Zoe) (2014)
• The Yes Men (an adventure related by the characters Polly, Ben & Jamie) (2015)
• The Forsaken (an adventure related by the characters Polly, Ben & Jamie) (2015)
• The Black Hole (an adventure related by the characters Jamie & Victoria) (2015)
• The Isos Network (an adventure related by the characters Jamie & Zoe) (2015)
• The Night's Witches (an adventure related by the characters Polly, Ben & Jamie) (2017)
• The Outliers (an adventure related by the characters Polly, Ben & Jamie) (2017)
• The Morton Legacy (an adventure related by the characters Polly, Ben & Jamie) (2017)
• The Wreck of the World (an adventure related by the characters Jamie & Zoe) (2017)

Short Trips audios

• A Stain of Red in the Sand
• The Way Forward
• Seven to One
• The Five Dimensional Man
• Penny Wise, Pound Foolish

Novels and short stories

Virgin New Adventures

• Timewyrm: Apocalypse by Nigel Robinson (brief flashback to the Second Doctor's era; the Seventh Doctor also interacts with his 'memory' of his second incarnation's personality, manifesting to him via the TARDIS telepathic circuits)

Virgin Missing Adventures

• The Menagerie by Martin Day
• Invasion of the Cat-People by Gary Russell
• Twilight of the Gods by Christopher Bulis
• The Dark Path by David A. McIntee

Past Doctor Adventures

• The Murder Game by Steve Lyons
• The Roundheads by Mark Gatiss
• Dreams of Empire by Justin Richards
• The Final Sanction by Steve Lyons
• Heart of TARDIS by Dave Stone (Also features the Fourth Doctor, although neither Doctor meets the other, each Doctor simply tackling a different end of the same crisis with only the Fourth aware of his other self's involvement)
• Independence Day by Peter Darvill-Evans (brief appearance only; predominately Seventh Doctor novel)
• Dying in the Sun by Jon de Burgh Miller
• Combat Rock by Mick Lewis
• The Colony of Lies by Colin Brake (brief interaction with the Seventh Doctor in a virtual reality)
• The Indestructible Man by Simon Messingham
• World Game by Terrance Dicks (depicts a possible beginning for the 'Season 6B' theory)

Eighth Doctor Adventures

• The Eight Doctors by Terrance Dicks
• Seen in the TARDIS mirror in Camera Obscura

Telos Doctor Who novellas

• Foreign Devils by Andrew Cartmel
• Wonderland by Mark Chadbourn

BBC Books

• The Wheel of Ice by Stephen Baxter

Penguin Fiftieth Anniversary eBook novellas

• The Nameless City by Michael Scott

Comics

TV Comic

• The Extortioners
• The Trodos Ambush
• The Doctor Strikes Back
• The Zombies
• Master of the Spiders
• The Exterminator
• The Monsters from the Past
• The TARDIS Worshippers
• Space War Two
• Egyptian Escapade
• The Coming of the Cybermen
• The Faithful Rocket Pack
• Flower Power
• The Witches
• Cyber-Mole
• The Sabre Toothed Gorillas
• The Cyber Empire
• The Dyrons
• Dr. Who and the Space Pirates
• Car of the Century
• The Jokers
• Invasion of the Quarks
• The Killer Wasps
• Ice Cape Terror
• Jungle of Doom
• Father Time
• Martha the Mechanical Housemaid
• The Duellists
• Eskimo Joe
• Perils at 60 Fathoms
• Operation Wurlitzer
• Action in Exile
• The Mark of Terror
• The Brotherhood
• U.F.O.
• The Night Walkers

TV Comic Specials

• Barnabus
• Jungle Adventures
• Return of the Witches
• Masquerade
• The Champion
• The Entertainer

TV Comic Annuals

• Attack of the Daleks
• Pursued by the Trods
• The Time Museum
• The Electrodes
• Death Race
• Test Flight

Doctor Who Magazine

• Land of the Blind

Doctor Who Magazine Specials

• Bringer of Darkness

IDW series

• The Forgotten
• Prisoners of Time