Little, who was forced to retire through injury, was coach of The Lions' Under-16 side in the FA Premier Academy League last season and at the age of 25, is one of the youngest coaches to be appointed at this level.
"I have worked with Joe for several years now, and he really is a very forward thinking young coach indeed" commented former Millwall captain Les Briley, who will become Little's assistant.
"He has some tremendous ideas about taking the Academy forward and I firmly believe that Joe's appointment is a very exciting one for this football club.
"In spite of his age, he already has considerable experience in all aspects of this job and is an excellent communicator. I'm really looking forward to the season now and we can promise the fans that we have some terrific young players coming through the Academy whom, I confidently predict, will flourish under Joe's guidance."