Farrell was diagnosed with Stage 1 lymphoma in August and stepped down as Boston's manager.
The team announced Sunday that Farrell will return to his position "provided a clean bill of health."
Farrell, who managed Boston to a World Series title in 2013, pitched for the Cowboys from 1981-1984, posting a 12-2 record his senior season. Farrell rejoined the program in 1997 as an assistant coach and left in 2001.