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Saharanpur city grew in a region named after a Sufi Saint Shah Haroon Chishti. It was founded by Sah Ranbirsingh, a Jain nobleman, who laid the foundations of the present-day city on the site of an army cantonment.

Saharanpur is declared as one amongst the 100 Smart Cities by MOUD as a part of Smart Cities Mission.

During the reign of Shamsu’d-Din Iltutmish (1211-36), the region became a part of the Delhi Sultanate. At that time, most of the area remained covered with forests and marshlands, through which the Paondhoi, Dhamola, and Ganda Nala rivers flowed. The climate was humid and malaria outbreaks were common. Muhammad bin Tughluq, the Sultan of Delhi (1325-1351), undertook a campaign in the northern ''doab'' to crush the rebellion of the Siwalik Hills kings in 1340, when according to local tradition he learned of the presence of a sufi saint on the banks of the Paondhoi River. After visiting the sage, he ordered that henceforth this region would be known as 'Shah-Haroonpur', after the Sufi Saint ''Shah Haroon Chishti''. The simple but well-preserved tomb of this saint is situated in the oldest quarter of Saharanpur city, between the Mali Gate/Bazar Dinanath and Halwai Hatta. By the end of 14th century, the power of the Sultanate had declined and it was attacked by Emperor Timur (1336-1405) of Central Asia. Timur had marched through Saharanpur region in 1399 to sack Delhi and people of the region fought his army unsuccessfully. A weakened Sultanate was later conquered by the Central Asian Mogul king Babur (1483-1531).

During the Mughal Empire, Akbar (1542-1605), Saharanpur became an administrative unit under the Province of Delhi. Akbar bestowed the feudal ''jagir'' of Saharanpur to the Mughal treasurer, Sah Ranveer Singh, an Agrawal Jain it is now known as the 'Digamber-Jain Panchayati Mandir'.

Mughal emperors Akbar and later Shah Jehan (1592-1666) bestowed the administrative ''pargana'' of Sarwat on Muslim Sayyid families. In 1633 one of them founded a city and named it and the surrounding region Muzaffarnagar, in honour of his father, Sayyid Muzaffar Ali Khan. The Sayyids ruled the area until the 1739 invasion by Nadir Shah. After his departure, anarchy prevailed across the entire ''doab'' with the region ruled

ravaged in succession by Rajputs, Tyagis, Brahmins, and Jats. Taking advantage of this anarchy, the Rohillas took control of the entire Trans-Gangetic region.

Ahmad Shah Durrani, the Afghanistan ruler who invaded Northwestern and Northern India in the 1750s, conferred the territory of Saharanpur as Jagir on Rohilla chief Najaf Khan, who assumed the title of Nawab Najeeb-ud-Daula and took up residence in Saharanpur in 1754. He made Gaunsgarh his capital and tried to strengthen his position against Maratha Empire attacks by entering an alliance with the Hindu Gurjar chieftain Manohar Singh. In 1759, Najeeb-ud-Daula issued a Deed of Agreement handing over 550 villages to Manohar Singh, who became the Raja of Landaura. Thus the Rohillas and the Gurjars now controlled Saharanpur.

In 1757, the Maratha army invaded the Saharanpur region, which resulted in Najeeb-ud-Daula losing control of Saharanpur to the Maratha rulers Raghunathrao and Malharao Holkar. The conflict between Rohillas and Marathas came to an end on 18December 1788 with the arrest of Ghulam Qadir, the grandson of Najeeb-ud-Daula, who was defeated by the Maratha general Mahadji Scindia. The most significant contribution of Nawab Ghulam Qadir to Saharanpur city is the Nawab Ganj area and the Ahmedabadi fortress therein, which still stands. The death of Ghulam Qadir put an end to the Rohilla administration in Saharanpur and it became the northernmost district of the Maratha Empire. Ghani Bahadur Banda was appointed its first Maratha governor. The Maratha Regime saw the construction of the Bhuteshwar Temple and Bagheshwar Temple in Saharanpur city. In 1803, following the Second Anglo-Maratha War, when the British East India Company defeated the Maratha Empire, Saharanpur came under British suzerainty.

In 1845 Nawab Rao Wazir-ud-din khan became the member and voter of mughal darbar at Red fort Delhi due to his corridal relation with Mugal Emperor Bahadur Shah Zafar. He was the richest person of district Saharanpur with 52 thousand bega land and lord of 57 village's like shaikhpura, landohra, tapri, piragpur, yousfpur, badshapur, harhati, nazirpura, santgarh, lakhnor, subri, pathri etc., of district Saharanpur. British governor's had good relation with Rao Wazir-ud-din and title Badsha-e-waqt (the king of his Period ) was bestowed to him. He died in 1895 at Sheikpura Qudeem (Saharanpur). He had two son's Nawab Rao Mashooq Ali khan and Nawab Rao Ghafoor Muhammad ali khan. Rao Ghafoor Muhammad ali khan had only seven children out of seven his elder son Nawab Rao Maqsood Ali khan was a great person. He was highly educated. He got his education from Aligarh Muslim University and University of Oxford. He was an intellectual and a spiritual person. Due to his kindness and amiable nature he's was popular among people's. He proved his resourcefulness and abilities by saving poor from famine and loss of crops. He became the disciple of Sufi Hazart Sheik Bahauddin a descendant of Tipu Sultan. He spread Sufism across the Saharanpur region. He was a great scholar and Many books in English and Persian were written by him but all his work lost after his death. He was a great Nawab of Saharanpur. He was the lord of a large property in Saharanpur region and in Dehradun. He worked for the welfare and upliftment of people and donated to poor farmers and land for Madarsa's and Darga's. Due to his Phalinthrophist work Nawab Maqsood Ali khan was awarded by the Viceroy of India Lord Irwin at Dehradun. Brother's of him migrated to Pakistan and England. He died in 1973 at sheikpura qudeem and left behind his sons Nawab Rao Ghulam muhi-ud-din khan, Nawab Rao Zamir haider khan, Nawab Rao yaqoob khan. Nawab Rao Gulam Hafiz khan.Nawab Rao Zamir Haider Son Prince Shameem Hyder Rao is a Fashion Model and a Poet.

The Saharanpur Botanical Gardens, known as the Company Garden and once the preserve of the British East India Company, is one of the oldest existing gardens in India, dating to before 1750. Then named Farahat-Bakhsh, it was originally a pleasure ground set out by a local chief, Intazam ud-ullah. In 1817, it was acquired by the British East India Company and placed under the authority of the District Surgeon. Joseph Dalton Hooker says of this Botanical Garden that "Amongst its greatest triumphs may be considered the introduction of the tea-plant from China, a fact I allude to, as many of my English readers may not be aware that the establishment of the tea-trade in the Himalaya and Assam is almost entirely the work of the superintendents of the gardens of Calcutta and Seharunpore. In 1887, when the Botanical Survey of India was set up to reform the country's botany, Saharanpur became the centre for the survey of the northern Indian flora. The Garden is seen historically as being second only to the Indian Botanical Gardens for its contribution to science and economy in India. Under private auspices today, it is full of greenery and has many different kinds of plants and flowers.

Saharanpur falls on the route of the proposed Dedicated Freight Corridor Corporation of India project, funded by the World Bank.