Its first office was started from the Nizam Guest House, which is part of Bhandarkar Oriental Research Institute on Law College Road.

[8] The institution's name was changed from the University of Pune to Savitribai Phule Pune University on 9 August 2014 in honor of Savitribai Phule, the 19th century Indian social reformer who played an important role in improving the lives of women and the Dalit communities in Maharashtra during British colonial rule.

She and her husband Mahatma Jyotiba Phule founded India's first native-run school for girls in 1848.

With the establishment of Shivaji University in Kolhapur in 1962, the jurisdiction was restricted to five districts: Pune, Ahmednagar, Nashik, Dhule, and Jalgaon.

[29] In science and engineering, notable alumni of the university include Padmanabhan Balaram, chemist and director of the Indian Institute of Science; Kantilal Mardia, statistician and Guy Medallists; Thomas Kailath, electrical engineer and recipient of the 2014 National Medal of Science; Vistasp Karbhari, civil engineer and the eighth president of the University of Texas at Arlington;[30] Suhas Patankar, professor at the University of Minnesota, and pioneer in the field of computational fluid dynamics (CFD) and finite volume method; C. Kumar N. Patel, inventor of the carbon dioxide laser, recipient of the 1996 National Medal of Science and vice-Chancellor for Research at the University of California, Los Angeles;[31] and Vinod Scaria, bioinformatician, who is known for sequencing the first Indian genome.

Politician includes Agatha Sangma, K. T. Rama Rao,[32] Prakash Javadekar, and Nabeel Rajab.

[35] Journalist Shereen Bhan received her master's in Communication Studies, with film and television as her areas of specialisation from the university.