Jesse Levine and Michael Shabaz were the defending champions, but both players were no longer eligible to compete in the juniors.

Kellen Damico and Nathaniel Schnugg defeated Martin Kližan and Andrej Martin in the final, 7–6^(9–7), 6–2 to win the boys' doubles tennis title at the 2006 Wimbledon Championships.^[1]

	Semifinals							Final
		Kellen Damico Nathaniel Schnugg	6	3	6
		Nikola Mektić Vedran Šiljegović	3	6	0
									Kellen Damico Nathaniel Schnugg	79	6
								2	Martin Kližan Andrej Martin	67	2
		Lee Hsin-han Rupesh Roy	3	77	3
	2	Martin Kližan Andrej Martin	6	64	6

	First round							Second round							Quarterfinals							Semifinals
	1	Thiemo de Bakker Alexandre Sidorenko	4	6	5
		Kellen Damico Nathaniel Schnugg	6	3	7				K Damico N Schnugg	3	6	6
		Thomas Fabbiano Daniel Alejandro López	6	66	3				B Klein J-P Smith	6	3	4
		Brydan Klein John-Patrick Smith	4	78	6											K Damico N Schnugg	63	6	6
		Kevin Botti Dylan Sessagesimi	65	4												G Elias P Sousa	77	4	3
	WC	David Rice Darren Walsh	77	6				WC	D Rice D Walsh	1	4
		Gastão Elias Pedro Sousa	2	7	9				G Elias P Sousa	6	6
	8	Jaak Põldma Ivan Sergeyev	6	5	7																		K Damico N Schnugg	6	3	6
	4	Jeevan Nedunchezhiyan Sanam Singh	64	4																			N Mektić V Šiljegović	3	6	0
		Nikola Mektić Vedran Šiljegović	77	6					N Mektić V Šiljegović	6	6
		Bai Yan Nicolas Santos	7	3	5				F Aidil J Xu	4	3
		Faisal Aidil Xu Junchao	5	6	7											N Mektić V Šiljegović	6	6
		Dennis Lajola Christian Vitulli	6	6												D Lajola C Vitulli	4	4
	WC	Daniel Cox Graeme Dyce	2	3					D Lajola C Vitulli	7	1
	WC	Fernando Romboli Daniel Dutra da Silva	4	6	6			WC	R Romboli D Dutra da Silva	5	0r
	7	Philip Bester Robin Roshardt	6	4	4

	First round							Second round							Quarterfinals							Semifinals
	5	Sho Aida Artur Chernov	6	3	4
		Edgar Rodriguez José Roberto Velasco	1	6	6				E Rodriguez JR Velasco	77	3	4
		Lee Hsin-han Rupesh Roy	6	6					H-h Lee R Roy	62	6	6
	WC	Scott Dickson Christopher Llewellyn	2	3												H-h Lee R Roy	77	64	6
		Bassam Beidas Marcin Gawron	1	4											3	L Belić A Veić	65	77	4
		Jamie Hunt Roberto Maytín	6	6					J Hunt R Maytín	2	6	2
		Greg Jones James Lemke	7	4	4			3	L Belić A Veić	6	2	6
	3	Luka Belić Antonio Veić	5	6	6																		H-h Lee R Roy	3	77	3
	6	Roman Jebavý Hans Podlipnik-Castillo	4	1																		2	M Kližan A Martin	6	64	6
		Stephen Donald Michal Konečný	6	6					S Donald M Konečný	66	77	7
		Błażej Koniusz Grzegorz Panfil	5	4					J Garrapiz-Borderías A Ramos Viñolas	78	64	9
		Javier Garrapiz-Borderías Albert Ramos Viñolas	7	6												J Garrapiz-Borderías A Ramos Viñolas	4	3
		Peter Lucassen Petru-Alexandru Luncanu	w/o												2	M Kližan A Martin	6	6
		Pavel Chekhov Emiliano Massa							P Lucassen P-A Luncanu	65	2
		Paris Gemouchidis Ricardo Urzúa Rivera	5	5				2	M Kližan A Martin	77	6
	2	Martin Kližan Andrej Martin	7	7

• Source for the draw at Wimbledon.com
• "The Junior Championships, Wimbledon 2006". International Tennis Federation. Retrieved 29 May 2018.