The FIFA World Cup in Qatar starts in less than three weeks and an injury at this stage all but ends the 25-year-old’s chances of participating in the tournament.
Denis Zakaria scored the winner as the London side came from a goal down to defeat Croatian champions. However, the victory was marred by Chilwell’s injury in stoppage time.
“It doesn’t look positive. It’s a hamstring,” said Chelsea boss Graham Potter.
“We will have to scan it and see how it is.”
Ben Chilwell has 17 caps for England and was on course to make Gareth Southgate’s final team for the Mundial.
Debutant Denis Zakaria had this to say after scoring the winner at Stamford Bridge.
“I have to say, (it’s been) very, very difficult,” Zakaria told BT Sport. “I like to play and always want to play.
“When you have to see your teammates from the bench it is not easy but I was always behind the team and was waiting for my chance. Today it came and I took my chance.”