The Maratha king Shivaji Maharaj commissioned Moropant Trimbak Pingle, his prime minister, to undertake the construction of this fort in order to defend the banks of the Nira and the Koyna rivers, and to defend the Par pass. It was completed in 1656. The Battle of Pratapgarh between Shivaji and Afzal Khan was fought below the ramparts of this fort on November 10, 1659. This was the first major test of the fledgling kingdom's army, and set the stage of the establishment of the Maratha empire. Pratapgad continued to be involved in regional politics. Sakharam Bapu, a well-known minister of Pune, was confined by his rival Nana Phadnis in Pratapgad in 1778.
He was later moved from fort to fort until he died at Raigad. In 1796, Nana Phadnis, while escaping from the intrigues of Daulatrao Shinde and his minister Baloba, assembled a strong garrison in Pratapgad before heading to Mahad. In 1818, as part of the Third Anglo-Maratha War, Pratapgad surrendered by private negotiation. This was a great loss to the Maratha forces, as Pratapgad was an important stronghold, had a large garrison, and could suppress much of the country around Wai.
A 17 feet high equestrian bronze statue of Shivaji was unveiled by Jawaharlal Nehru, then Prime Minister of India, on the 30th of November 1957, the same year a road was constructed by the Public Works Department from Kumbhrosi village up to fort. A guest house and a national park were built inside the fort in 1960. The fort is currently owned by Uday Raje Bhosale, the heir to the former Satara princely state.