The X Factor winner will perform Michael Jackson's 'She's Out of My Life' in Thriller Live on November 15.
Headliner Macy Gray and girl group Stooshe will also each separately take on a Michael Jackson classic in Thriller Live.
McElderry said: "I am so excited to be performing in such an acclaimed West End musical, celebrating the King of Pop - Michael Jackson.
"To be able to sing my own version of 'She's Out of My Life' is such an honour and even more so to be involved in BBC Children in Need. I can't wait!"
'POP Goes the Musical' allows celebrities to give one-off performances in West End musicals to help raise vital funds for disadvantaged children and young people in the UK.
Geri Halliwell, Alexandra Burke and Blue are also part of this year's effort. Halliwell will appear in Singin' in the Rain on October 25, while the others have already taken to the stage.
Tickets can be purchased at www.lastminute.com/pudsey, with 50% of the ticket price going to BBC Children in Need.