All-rounder Stokes felt a tight hamstring in fielding practice on Wednesday at Headingley and was limited to shuttle runs with the team physio yesterday, despite reporting a slight improvement.
Stokes will undergo a scan to try to assess the extent of the injury and is likely to face a late fitness test before England name their side.
Uncapped Surrey seamer Sam Curran, 19, has been called up as cover.
“Of course if Ben’s fit we want him in the side, he’s one of our best players, he brings a lot to the table and offers so much to this team,” Root said.
Pakistan won the first Test by nine wickets at Lord’s last week and Root believes a quick return to action will benefit his side.
“I think it helps us getting straight back into it, not having too much time to think about things,” Root said.
“It was very clear where we needed to improve from last week. We’ve had some good preparation, the guys have really worked hard and now it’s just doing it, going out and proving a point, putting a really strong performance in as a group and showing some pride in the badge.”
Lancashire opener Keaton Jennings returns to the side to partner Alastair Cook at the top of the order and Root added: “He will be desperate to take his opportunity. Every player in this side wants to make an impact this week.
“Every time we play a Test match there are all sorts of different pressures that come with it and for Keaton it’s a great opportunity. I hope he looks at it that way and goes out and expresses himself in his own way.”
Asked if he was feeling the pressure of arresting England’s poor run of form, Root said: “When you are winning and performing well you have to keep churning out those performances and when you’re on the other side of it you’ve got to make sure you turn it round.
“As always, I’ve gone into practice, felt if there were any areas I wanted to work on and got them done so I can go in full of confidence tomorrow and know I’ve given myself the best chance. It’s nice to have that feeling going into any game.”