The 18-year-old defender is in the final three with Hakeem Odoffin (Wolves) and Ben Godfrey (Norwich City).
Musonda, who signed his first professional deal back in November, was handed his first team debut by new boss Nathan Jones in the closing stages of the 2-0 win at Mansfield in January.
Drew Barrand, Marketing Director of The Football League, said: “The Football League Awards 2016 provides a platform for us to showcase the very best of what The Football League is all about.
“Once again, the standard of entries has gone up so those clubs and individuals included on the shortlists deserve real praise for their achievements.
“We wish all those nominated the best of luck and look forward to announcing the winners in April at what will be the first ever Football League Awards evening to be held in Manchester.”