Doctors found the embolism, which occurs when the main artery of the lung or one of its branches becomes blocked, during the course of all the testing Jenks had on his back.
"Bobby's doing fine, and he's on the proper medication. He's doing great," Francona said.
Jenks, who remains with the team, is shut down from all physical activities for the foreseeable future, according to Francona. Francona reiterated, however, that this situation would not end the pitcher's career.
"I don't believe so," he said. "It's not something to mess around with, but it was a very small embolism and they have it under control. Certainly they want it to go away, but I they feel like he's in good shape."
Jenks has made three trips to the disabled list this season, twice because of back tightness. The right-handed reliever is 2-2 with a 6.32 ERA in 19 appearances this season, his first with Boston after six seasons with the White Sox.
"It's certainly nothing to mess around with, there just needed to be a lot of testing," Francona said. "Bobby was put on the proper medication, and that's probably going to slow down the efforts to look at his back a little bit, but in a hurry the back becomes secondary."
Joe McDonald covers the Red Sox for ESPNBoston.com.