Pfau was undergoing treatment at a hospital since two weeks and passed away during a surgery at 12.30 a.m., Dawn newspaper reported.
She has been running a leprosy centre and was in charge of Mary Adelaide Society of Pakistan, where leprosy patients are treated.
The funeral was scheduled for August 19 in Karachi, said Shariq Zaman, a spokesman for Pfau's charity.
Hailing from Germany, Dr Pfau had been staying in Pakistan since 1960, when she was just 29, dedicating her life to cure patients of leprosy.
"She gave new hope to innumerable people and proved through her illustrious toil that serving humanity knows no boundaries", the statement said.
She started to set up clinics across Pakistan after visiting the country in 1960 and witnessing leprosy for the first time. After her graduation she joined the religious order fo the Daughters of the Heart of Mary, which sent her on mission to India. "Pakistani nation salutes Dr. Pfau and her great tradition to serve humanity will be continued", the President stated.
Not required to take the veil or live in seclusion, she ended up in Pakistan by chance. By 1996, the World Health Organization declared that leprosy had been controlled in Pakistan. En route to work in India, visa complications forced her to break the journey in Karachi, where she visited a lepers' colony.
In collaboration with the government Pfau expanded leprosy treatment centres in more than 150 cities and towns across Pakistan, training doctors, treating thousands of victims and helping establish a national programme to bring the disease under control.
And she received a number of honors, including, in 1979, Pakistan's second highest civilian award: the Hilal-e-Imtiaz; in 1989 she received the Hilal-e-Pakistan and the German Staufer Medal in 2015.
Her last ceremonies will be performed on August 19 at St. Patrick's Church in Karachi's Saddar area. "We owe u a debt of gratitude Dr Ruth Pfau".