Madugalle, who played 21 Tests and 63 One-day matches and also captained his country, is a well-respected ICC referee.
The 44-year-old has served as an ICC Match Referee since 1994 and has officiated in matches involving all Test playing nations.
The PCB has also named a panel of local umpires who will stand beside ICC neutral umpires in the five-match One-day series, which starts in Karachi on March 13.
Australian Simon Taufel and English veteran David Shepherd will stand in the One-day series, while West Indian Steve Bucknor and South African Rudi Koertzen will join the two for the three-match Test series.
India arrives in Lahore on March 10 for their first tour of Pakistan in 15 years.