Dr. Hans-Wilhelm Muller-Wohlfahrt has told Sport Bild that returning to Bayern Munich is "like coming back to a family."
He had also briefly left in 2008 following a dispute with then coach Jurgen Klinsmann before returning the following year after Jupp Heynckes, now back in charge, had taken over.
"I'm happy to be back at Bayern -- it's like coming back to a family. I'm delighted to be working again at the club where I was employed for so long," Muller-Wohlfahrt said.
"I'll be on the bench for every Champions League game, home and away, and definitely for the DFB Pokal game against Dortmund."
Muller-Wohlfahrt comes back after the resignation of Dr. Volker Braun as first-team doctor earlier this month.
Bild reported that Braun had not applied "ideal treatment methods," meaning injured players such as Manuel Neuer spent extended spells on the sidelines.
However, Bayern captain Neuer said the doctor was "absolutely not to blame."
Club president Uli Hoeness told Merkur that Muller-Wohlfahrt would head Bayern's medical team. The club plan to open a practice at their Sabener Strasse training centre next year, at which he will act as a "supervisor" to younger doctors.
"I'll attend Sabener Strasse every day until the end of the year," Muller-Wohlfahrt, who is also the Germany national team doctor, said. "I want to give myself a clear picture of every individual player."
Muller-Wohlfahrt had continued to treat Bayern stars including Arjen Robben, Jerome Boateng and Robert Lewandowski even when he was not officially on the club's payroll.