The right-hander will undergo an MRI on Tuesday to see if this is related to a muscle strain from April.
Fujikawa pitched 1 2-3 scoreless innings in a victory over Cincinnati on Sunday before leaving with the injury.
The Cubs replaced Fujikawa on the roster by claiming reliever Alex Burnett off waivers from Baltimore.
The 32-year-old Fujikawa is 1-1 with a 5.25 ERA this season, although he has 14 strikeouts in 12 innings. The Japanese reliever signed a two-year contract for $9.5 million with the Cubs in the offseason.