Roger Federer and Olivier Rochus were the defending champions, but they did not compete in the Junior's this year.

Guillermo Coria and David Nalbandian defeated Todor Enev and Jarkko Nieminen in the final, 7–5, 6–4 to win the boys' doubles tennis title at the 1999 Wimbledon Championships.^[1]

	Semifinals							Final
	1	Guillermo Coria David Nalbandian	3	7	17
		Mark Hilton James Nelson	6	5	15
								1	Guillermo Coria David Nalbandian	7	6
									Todor Enev Jarkko Nieminen	5	4
		Todor Enev Jarkko Nieminen	7	6
	2	José de Armas Daniel Langre	6	2

	First round							Second round							Quarterfinals							Semifinals
	1	Guillermo Coria David Nalbandian	7	7
		Jordan Gray Tom Higgins	5	6				1	G Coria D Nalbandian	6	6
		Alan Mackin Matthew Trudgeon	6	6					A Mackin M Trudgeon	3	4
		Thiago Alves Timo Nieminen	2	1											1	G Coria D Nalbandian	7	6
		Levar Harper-Griffith Andy Roddick	7	6											5	L Childs S Dickson	6	4
		Cătălin-Ionuț Gârd Roko Karanušić	6	3					L Harper-Griffith A Roddick	4	4
		Richard Brooks Nick Greenhouse	4	2				5	L Childs S Dickson	6	6
	5	Lee Childs Simon Dickson	6	6																		1	G Coria D Nalbandian	3	6	17
	4	Julien Benneteau Nicolas Mahut	6	4	10																		M Hilton J Nelson	6	5	15
		Matias Ormaza de Paul Cristian Villagrán	0	6	8			4	J Benneteau N Mahut	6	6
		Andrew Banks Benjamin Riby	7	6					A Banks B Riby	1	3
		Aleksandar Vlaški Brandon Weir-Smith	6	4											4	J Benneteau N Mahut	6	6	1
		Mark Hilton James Nelson	7	6												M Hilton J Nelson	7	3	6
		Ryan Russell Wayne Wong	6	3					M Hilton J Nelson	6	6
		Tres Davis Alberto Francis	6	4				6	J Johansson L Zovko	4	4
	6	Joachim Johansson Lovro Zovko	7	6

	First round							Second round							Quarterfinals							Semifinals
	7	Ladislav Chramosta Jakub Hašek	6	6	6
		Fred Hemmes Jr. Luben Pampoulov	7	4	2			7	L Chramosta J Hašek	4	2
		Michael Lammer Renaud Thys	3	1					T Enev J Nieminen	6	6
		Todor Enev Jarkko Nieminen	6	6												T Enev J Nieminen	7	7
		Andrew Anderson Dirk Stegmann	6	6											3	J Melzer K Pless	6	6
		Robert Green Mark Weaver	4	4					A Anderson D Stegmann	4	2
		Steve Berke Dirk Britzen	3	4				3	J Melzer K Pless	6	6
	3	Jürgen Melzer Kristian Pless	6	6																			T Enev J Nieminen	7	6
	8	Todd Martin Jean-Julien Rojer	7	6																		2	J de Armas D Langre	6	2
		Karol Beck Stephen Nugent	6	2				8	T Martin J-J Rojer	4	6	9
		Mario Ančić Andrej Kračman	6	3	4				H Furukawa Y Miyazaki	6	1	7
		Hayato Furukawa Yasuo Miyazaki	4	6	6										8	T Martin J-J Rojer	1	5
		Jean-Christophe Faurel Éric Prodon	6	1	1										2	J de Armas D Langre	6	7
		Alex Bogomolov Jr. John Paul Fruttero	3	6	6				A Bogomolov Jr. J-P Fruttero	6	6
		Phillip Harboe Andrew McDade	4	3				2	J de Armas D Langre	7	7
	2	José de Armas Daniel Langre	6	6

• Source for the draw at Wimbledon.com
• "The Junior Championships, Wimbledon 1999". International Tennis Federation. Archived from the original on 3 May 2018. Retrieved 3 May 2018.