Makhanya takes over the reins after a successful World Cup campaign where the South Africans lifted the trophy in Dubai in March.
Makhanya and Andile Phehlukwayo were the only two remaining players from that squad.
“This is a dream come true,” Makhanya said in a statement.
“Every young boy dreams of representing the green and gold and to be asked to captain the squad too means so much more to me. I’m grateful for the opportunity to prove myself and excited to lead the team going to England.
“We have a really good group of guys going and they are all eager to give their best. I will definitely give this job by very best and look forward to flying the South African flag high.”
The announcement was made after new coach Lawrence Mahatlane named his 15-man squad for the tour, following a four-day national camp in Pretoria.
“I’m really happy with the team that has been selected,” Mahatlane ahead of his first tour in charge of the junior national team.
The under-19 squad would travel to England on July 23 for a month-long tour, where they take part in a two-match Test series and a five-match ODI series.
“It is an exciting mixture of players with a lot of all-rounders coming through, which is always good.
“The camp was a huge success and I’m happy to see the guys taking on their learnings so quickly. This tour to England will be a good opportunity for us to measure ourselves against one of the top teams in the world and begin that long trek to defending the World Cup title.”
SA under-19 squad: Sibonelo Makhanya (captain), Marques Ackerman, Aiden Brooker, Matthew Christensen, Keith Dudgeon, Brandon Glover, Stefan Klopper, Janneman Malan, Ndumiso Mvelase, Hanco Olivier, Andile Phehlukwayo, Ryan Rickleton, Grant Roelofsen, Kabelo Sekhukhune, Lwandiswa Zuma.