Jyothirao Govindrao Phule was born in 1827 into a family that belonged to the Mali caste, traditionally occupied as gardeners and considered to be of the shudra varna in the ritual ranking system of Hinduism. The original surname of the family had been Gorhe and had its origins in the village of Katgun, in present day Satara District, Maharashtra. Phule's great-grandfather worked as a chaugula, a lowly type of village servant, in that village but had to move to Khanwadi in Poona district after murdering a Brahmin with whom he had a dispute. He prospered there but his only son, Shetiba, who was of poor intelligence, subsequently squandered what had been gained. Shetiba moved himself and his family, including three boys, to Poona in search of some form of income. The boys were taken under the wing of a florist, who taught them his trade. Their proficiency in growing and arranging became well known and they adopted the name of Phule (flower-man) in place of Gorhe. Their fulfilment of commissions from the Peshwa, Baji Rao II, for flower mattresses and other goods for the rituals and ceremonies of the royal court so impressed him that he granted them 35 acres (14 ha) of land on the basis of the inam system, whereby no tax would be payable upon it. The oldest brother machinated to take sole control of the property, leaving the younger two siblings, including Jyotirao Phule's father, Govindrao, to continue farming and flower-selling.

Govindrao married Chimnabai and had two sons, of whom Jyotirao was the younger. Chimnabai died before he was aged one. The Mali community did not set much store by education, and after attending primary school to learn the basics of reading, writing and arithmetic, Jyotirao was withdrawn from school. He joined the menfolk of his family at work, both in the shop and the farm. However, a Christian convert from the same Mali caste as Phule recognised his intelligence and persuaded Phule's father to allow Phule to attend the local Scottish Mission High School. Phule completed his English schooling in 1847. As was customary, he was married young, at the age of 13, to a girl of his own community, chosen by his father.

In 1848, aged 23, Phule visited the first girls' school in Ahmadnagar, run by Christian missionaries. It was also in 1848 that he read Thomas Paine's book Rights of Man and developed a keen sense of social justice. He realised that lower castes and women were at a disadvantage in Indian society, and also that education of these sections was vital to their emancipation.

To this end and in the same year, Phule first taught reading and writing to his wife, Savitribai, and then the couple started the first indigenously-run school for girls in Pune. Ostracised for this by their family and community, their friend Usman Sheikh and his sister Fatima Sheikh provided them their home to stay. They also helped to start the school in their premises. Later, the Phules started schools for children from the Mahar and Mang castes, which were both considered to be untouchable. In 1852, there were three Phule schools in operation but by 1858 they had all ended. Eleanor Zelliot blames the closure on private European donations drying up due to the Mutiny of 1857, withdrawal of government support, and Jyotirao resigning from the school management committee because of disagreement regarding the curriculum. He championed widow remarriage and started a home for pregnant Brahmin widows to give birth in a safe and secure place in 1863. His orphanage was established in an attempt to reduce the rate of infanticide. Phule tried to eliminate the stigma of social untouchability surrounding the lower castes by opening his house and the use of his water-well to the members of the lower castes.

On 24 September 1873, Phule formed Satyashodhak Samaj to focus on rights of depressed classes. Through this he opposed idolatry and denounced the caste system. Satyashodhak Samaj campaigned for the spread of rational thinking and rejected the need for Priests. Savitribai became the head of the women's section, which included ninety female members. After Phule's death in 1890 his followers continued the Samaj campaign in the remote parts of Maharashtra.

Phule was appointed commissioner (municipal council member) to the then Poona municipality in 1876 and served in this unelected position until 1883.

Apart from his role as a social Activist, Phule was a businessman too. In 1882 he styled himself as a merchant, cultivator and municipal contractor. He owned 60 acres (24 ha) of farmland at Manjri, near Pune.. For period of time, he worked as a contractor for the government and supplied building materials required for the construction of a dam on the Mula-Mutha river near Pune in the 1870s. He also received contracts to provide labour for the construction of the Katraj Tunnel and the Yerawda Jail near Pune. One of Phule's businesses, established in 1863, was to supply metal-casting equipment.

At an education commission hearing in 1884, Phule called for help in providing education for lower castes. To implement it, he advocated making primary education compulsory in villages. He also asked for special incentives to get more lower-caste people in high schools and colleges.

According to Dhananjay Keer, Phule was bestowed with the title of Mahatma on 11 May 1888 by another social reformer from Bombay, Vithalrao Krishnaji Vandekar.

An early biography of Phule was the Marathi-language Mahatma Jotirao Phule yanche charitra (P. S. Patil, Chikali: 1927), which has to be treated with caution because its author was an Activist. Two others are Mahatma Phule. Caritra Va Kriya (Mahatma Phule. Life and Work) (A. K. Ghorpade, Poona: 1953), which is also in Marathi, and Mahatma Jyotibha Phule: Father of Our Social Revolution (Dhananjay Keer, Bombay: 1974). Unpublished material relating to him is held by the Bombay State Committee on the History of the Freedom Movement.

He is credited with introducing the Marathi word dalit (broken, crushed) as a descriptor for those people who were outside the traditional varna system. The terminology was later popularised in the 1970s by the Dalit Panthers.