Obi was substituted on seven minutes with a head injury after a driven ball cannoned into him.
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The teen spent several minutes on the pitch being treated by United's medical staff, though was able to walk off unaided and speak with manager Adam Lawrence before being ushered to the dressing room.
Obi faces scans today as United seek to assess the injury.
The U21s are next back in action against Birmingham on Friday evening ahead of a clash with Southampton.
Goals from Shumaira Mheuka and Leo Cardoso saw Chelsea win 2-0 on Monday night.