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Pratap was born to the Thenua gotra Jat Hindu "princely family of state of Mursan in the Hathras District of Uttar Pradesh" on 1 December 1886. He was the third son of Raja Ghanshyam Singh. At the age of three, Raja Harnarayan Singh of Hathras adopted him as his son. He was married to Balveer Kaur belonging to a Jat Sikh family of Jind princely state of Haryana (then in Punjab) in 1902 while studying in college. She died in 1925.
In 1895 Pratap was admitted to the Government High School in Aligarh, but soon he switched over to the Muslim Anglo-Oriental Collegiate School. Here he received his education under British Headmasters and Muslim teachers all from Mohammedan Anglo Oriental College Aligarh founded by Sir Sayed Ahmad Khan. With this background he shaped into a true representative of secular society. To bring India to a par with European countries, Pratap established the free indigenous technical institute Prem Mahavidyalaya in his palace at Vrindavan on 24 May 1909.
In spite of objections from his father-in-law, Pratap went to Kolkata in 1906 to attend the Congress session, and met several leaders involved in the Swadeshi movement, deciding to promote small industries with indigenous goods and local artisans. He was very much against social evils, especially untouchability. To eliminate this evil he dined with a Tamata family of Almora in 1911, and a Mehtar[disambiguation needed] family of Agra in 1912. He was influenced by the speeches of Dadabhai Naoroji, Bal Gangadhar Tilak, Maharaja Baroda, and Bipin Chandra Pal, helping to make him a patriot who turned Swadeshi. He started the movement to burn the foreign-made clothes in his state.
After trying sincerely to liberate his motherland, on 20 December 1914 at the age of 28 Pratap left India for the third time, with a desire to liberate India from the clutches of British colonial rule by obtaining outside support.
In January 1915 on learning about his presence in Switzerland, Chatto alias Virendranath Chattopadhyay of the newly founded Berlin Committee (Deutsche Verein der Freunde Indien) requested Von Zimmermann of the German foreign ministry to get Pratap invited to Berlin. Already Chatto had sent a first mission to Afghanistan led by the Parsi revolutionary Dada Chanji Kersasp.
Informed about Chatto's activities from Shyamji Krishnavarma and Lala Hardayal, Pratap insisted on meeting the Kaiser Wilhelm II personally; Chatto rushed to Geneva to tell Pratap of the Kaiser's eagerness to see him, and they went to Berlin together. Har Dayal, too, followed them. Decorating Pratap with the Order of the Red Eagle, the Kaiser showed his awareness of the strategic position of the Phulkian States (Jind, Patiala and Nabha), if India was invaded through the Afghan frontier.
According to Pratap's wish, he was taken to a military camp near the Polish border to gain a firsthand knowledge of army policies and functioning. On 10 April 1915 accompanied by the German diplomat Von Hentig, Maulavi Barkatullah and a few other members, Pratap left Berlin, with due credentials from the Kaiser.
In Vienna the delegation met the Khedive of Egypt who during a conversation with Pratap expressed his desire to see the end of the British Empire. On their way, in Turkey they had an excellent visit with Enver Pasha, son-in-law of the Sultan and Defense Minister, who appointed a trusted military officer to guide them. They were received by Rauf Bey with a detachment of 2000 soldiers at Ispahan. They reached Kabul on 2 October and were greeted by Habibullah, having a number of discussions.
Provisional Government of India
On 1 December 1915 during World War I (his 28th birthday) Pratap established the first Provisional Government of India at Kabul in Afghanistan as a government-in-exile of Free Hindustan, with himself as President, Maulavi Barkatullah as Prime Minister, and Maulavi Abaidullah Sindhi as Home Minister, declaring jihad on the British. Anti-British forces supported his movement, but because of obvious loyalty to the British, the Amir kept on delaying the expedition to overthrow British rule in India.
Due to his revolutionary ideas Pratap had a good relationship with Lenin, who invited him to Russia after its liberation and welcomed him. By this time he had become a real threat to British rule in India, and the British Government of India put a bounty on his head, attacked his entire estate, and declared him a fugitive, causing him to flee to Japan in 1925.
In Japan he published the 'World Federation Monthly Magazine' in 1929, trying his best to use the world war situations to free India. During Second World War he stayed at Tokyo in Japan and continued his movement from 'World Federation Centre' to free India from British rule. He formed the Executive Board of India in Japan in 1940 during Second World War. At last the British government relented and Raja Mahendra Pratap was permitted to come to India from Tokyo with respect. He was also nominated for the Nobel Peace Prize in 1932.
Back to India
After independence also he continued his struggle for transfer of power to the common man. His vision was that the Panchayat Raj was the only tool which can put real power in the hands of people and reduce corruption and bureaucratic hurdles. He was the president of Indian Freedom Fighters' Association and was also the president of All India Jat Mahasabha. He was a member of the second Lok Sabha in 1957–1962. He was elected as an independent candidate from Mathura constituency defeating Bharatiya Jana Sangh (which would later evolved into BJP) candidate and the future Prime Minister of India, Atal Bihari Vajpayee in the 1957 Lok Sabha Elections. 
He died on 29 April 1979.
- Bhattacharya, Abinash Chandra (1962). Bahirbharate Bharater Muktiprayas (in Bengali), Kalikata:Firma K.L.Mukhopadhyaya, pp. 9–24
- Contributions of Raja Mahendra Prata by Hakim Syed Zillur Rahman, International Seminar on Raja Mahendra Pratap & Barkatullah Bhopali|Maulavi Barkatullah, Barkatulla University, Bhopal, 1–3 December 2005.
- The Nomination Database for the Nobel Prize in Peace, 1901–1955
- Dr. Vir Singh (2004), My Life History: 1986-1979, Raja Mahendra Pratap, ISBN 81-88629-24-3
- "Mahendra Pratap (Raja)" in Dictionary of National Biography, 1974, Vol.III,pp10–11
- Les origines intellectuelles du mouvement d'indépendance de l'Inde (1893–1918) by Prithwindra Mukherjee, Paris, 1986 (PhD Thesis)
- Mahendra Pratap materials at the South Asian American Digital Archive (SAADA)