The area has a very long history with the 8th century Rashtrakuta era cave temple of Pataleshwar being the oldest man made structure in Pune.

Shivajinagar was earlier known as Bhambwade. Later it came to known as Bhamburde.It is believed that Chhatrapati Shivaji Maharaj came to the temple of Rokdoba in the village and rested in Shirole Wada of Shirole family. During the Peshwa era, a factory making handcrafted paper operated from Bhamburde.

During the Maratha Empire era, the Patil (Head) of the village were Bahirat (Patil) (बहिरट-पाटील) family and Sardar Shirole (Patil) (सरदार शिरोळे-पाटील) family who also were Sardar (Commanders, Warriors) in the Maratha army.

In the 19th century, Jangali Maharaj, a saint revered mostly by hindus, established his residence here. His memorial temple (Samadhi) is located in the area and the major road in Shivajinagar is named after him.

In 1891, the Inamdar of Bhamburda, Rajaram Naroji Shirole Patil leased 37 acres of land at the foot of Hanuman hill for 99 years to the Deccan Education Society. The society's most well known institution, Fergusson College was built on this land.

After independence, the name of Bhamburde was changed to Shivajinagar. In early part of the 20th century, one of the oldest slums in Pune called Wadarwadi, initially occupied mostly by the nomadic Wadar community came into being on unused land of the Bahirat, Shirole and Ranade families close to the Chaturshrungi Temple.

In 1928, a statue of Chhatrapati Shivaji Maharaj was inaugurated on the grounds donated by the Shirole family. The Shri Shivaji military preparatory school was later built in the surrounding area.