Stokes suffered the injury two months ago and was forced to sit out the three-match home series against Sri Lanka and the first Pakistan Test last week.
Durham seamer Matt Potts also returns to the side for the first time since the Lord's Test against Sri Lanka at the end of August.
Seamers Gus Atkinson and Chris Woakes are rested.
England won the first Pakistan Test, also in Multan, by an innings and 47 runs on Friday, with Ollie Pope leading the side in Stokes's absence.
England rode on a brilliant 317 from Harry Brook and 262 from Joe Root for a stunning victory.
Pakistan became the first team in Test cricket's 147-year history to lose by an innings after posting a 550-plus total in the first innings.
England XI for second Test:
Ben Stokes (captain), Zak Crawley, Ben Duckett, Ollie Pope, Joe Root, Harry Brook, Jamie Smith, Brydon Carse, Matt Potts, Jack Leach, Shoaib Bashir
