The 18-year-old was forced off with an injury in the first half of Dortmund' 2-0 Bundesliga win against Werder Bremen on Saturday and he has emerged as a doubt for the visit of their Premier League counterparts.
Marius Wolf and Abdoulaye Kamara are two players who will definitely miss Wednesday's clash with respective shoulder and knee injuries, while Mateu Morey is struggling with fitness issues and is not expected to be involved.
Should Moukoko not be deemed fit to start, Sebastien Haller will likely get the nod up front, and the Ivorian - who has recently returned to the first-team fold after battling testicular cancer - could be supported in attack by Julian Brandt, Marco Reus and Karim Adeyemi, the latter of whom is available after serving a Bundesliga suspension last time out.
After recovering from a muscle strain, Thomas Meunier came on as a late substitute against Bremen, and the Belgian right-back will be pushing to start ahead of January signing Julian Ryerson.
Experienced centre-back Mats Hummels could return at the expense of either Niklas Sule or Nico Schlotterbeck, while star man Jude Bellingham - who has scored four goals in five Champions League games so far this season - is poised to start in centre-midfield alongside either Emre Can, Mahmoud Dahoud or Salih Ozcan.
Eighteen-year-old Englishman Jamie Bynoe-Gittens - who briefly spent time in Chelsea's academy - scored against Bremen less than two minutes after coming on as a substitute last weekend, but the forward is expected to begin on the bench on Wednesday.
Borussia Dortmund possible starting lineup: Kobel; Ryerson, Hummels, Schlotterbeck, Guerreiro; Bellingham, Can; Adeyemi, Reus, Brandt; Haller