It is hoped that using the boy's own tissue in the nine-hour operation at Great Ormond Street Hospital will cut the risk of rejection.
The world's first tissue-engineered windpipe transplant was done in Spain in 2008 but with a shorter graft.
Doctors say the boy is doing well and breathing normally.
He has a rare condition called Long Segment Congenital Tracheal Stenosis, in which patients are born with an extremely narrow airway.
At birth his airway was just one millimetre across.
Doctors had previously operated to expand his airway but in November last year he suffered complications from erosion of a metal stent in his windpipe or trachea.
In order to build him a new airway, doctors took a donor trachea, stripped it down to the collagen scaffolding, and then injected stem cells taken from his bone marrow.
The organ was then implanted in the boy and over the next month, doctors expect the stem cells to transform into specialised cells which form the inside and outside of the trachea.