Duffy faced three batters in the first inning and recorded two outs before catcher Humberto Quintero saw him shake out his arm at the end of a throw, prompting a mound visit from manager Ned Yost and a trainer.
"As soon as he said 'It's in my elbow,' I said 'That's it,'" Yost said. "We need to get that checked, see what's going on there, and go from there."
The 23-year-old Duffy was headed back to Kansas City on Sunday night. He also experienced tightness in his elbow last month.
"I think Q did the right thing. I felt a little tightness on the inner part of my elbow," he said. "You know, get an MRI tomorrow, check it out and see what it is. You can't worry about things like this until you know what it is."
Duffy is 2-2 with a 3.90 ERA in six starts this season.