The former Millwall defender, who last season ran the club's Under-18's side, will take charge of The Lions' youth set-up with immediate effect after Little decided to step-down from his role last week.
Speaking to the club's official website, manager Kenny Jackett made it clear that the development of young talent was a priority for the club.
"Over the past five years or so," he said. "There haven't been as many players progressing through the youth system here who have established themselves in the first team as perhaps there should have been and I'm determined to address that.
"No-one should be in any doubt that youth development remains at the top of the agenda at Millwall and I look forward with confidence to a successful period under Scott's leadership."