Youkilis was out of the starting lineup Friday for the start of a three-game series against Tampa Bay because of a hip injury.
"He was really limping the last couple days," Francona said. "The hip has started to bother him a little bit. Try to figure out what, where, why, so he hasn't have to limp the last couple weeks because we need him."
The Red Sox held a 6½-game lead entering Friday over Tampa Bay in the AL wild-card race. Youkilis returned from a lower back strain on Sept. 2.
"I think he's tolerated it real well," Francona said of Youlikis' back.
Also, pitcher Clay Buchholz, out with a lower back injury, threw at 120 feet and a schedule for when Buchholz could throw off a bullpen mound may be determined this weekend.
"The one thing we want him to do is go home from this season feeling good so he can pretty much have normal workouts," Francona said. "If he continues to do well though, pitching in our season has not been ruled out. That's kind of where we're at."
Right-hander Josh Beckett, who sprained his right ankle earlier this week, is also throwing and making progress. Left-hander Erik Bedard was examined in Boston and has a strained lat muscle, which probably happened after compensating for a sore knee.
John Lackey, Friday's starting pitcher, left after the third inning due to a bruised left calf. He was hit by John Jaso's two-out liner, but recovered to throw the Rays' catcher out at first base.