John Bunyan was born in 1628 to Thomas and Margaret Bunyan at Bunyan's End in the parish of Elstow, Bedfordshire. Bunyan's End is about halfway between the hamlet of Harrowden (one mile south-east of Bedford) and Elstow High Street. Bunyan's date of birth is not known, but he was baptised on 30 November 1628, the baptismal entry in the parish register reading "John the sonne of Thomas Bunnion Jun., the 30 November". The name Bunyan was spelt in many ways (there are 34 variants in Bedfordshire Record Office) and had its origins in the Norman-French name Buignon. There had been Bunyans in north Bedfordshire since at least 1199.

As a child Bunyan learned his father's trade of tinker and was given some rudimentary schooling. In Grace Abounding Bunyan recorded few details of his upbringing, but he did note how he picked up the habit of swearing (from his father), suffered from nightmares, and read the popular stories of the day in cheap chap-books. In the summer of 1644 Bunyan lost both his mother and his sister Margaret. That autumn, shortly before or after his sixteenth birthday, Bunyan enlisted in the Parliamentary army when an edict demanded 225 recruits from the town of Bedford. There are few details available about his military Service, which took place during the first stage of the English Civil War. A muster roll for the garrison of Newport Pagnell shows him as private "John Bunnian". In Grace Abounding, he recounted an incident from this time, as evidence of the grace of God:

Bunyan's army Service provided him with a knowledge of military language which he then used in his book The Holy War, and also exposed him to the ideas of the various religious sects and radical groups he came across in Newport Pagnell. The garrison town also gave him opportunities to indulge in the sort of behaviour he would later confess to in Grace Abounding: "So that until I came to the state of Marriage, I was the very ringleader of all the Youth that kept me company, in all manner of vice and ungodliness". Bunyan spent nearly three years in the army, leaving in 1647 to return to Elstow and his trade as a tinker. His father had remarried and had more children and Bunyan moved from Bunyan's End to a cottage in Elstow High Street.

Within two years of leaving the army, Bunyan married. The name of his wife and the exact date of his marriage are not known, but Bunyan did recall that his wife, a pious young woman, brought with her into the marriage two books that she had inherited from her father: Arthur Dent's Plain Man's Pathway to Heaven and Lewis Bayly's Practice of Piety. He also recalled that, apart from these two books, the newly-weds possessed little: "not having so much household-stuff as a Dish or a Spoon betwixt us both". The couple's first daughter, Mary, was born in 1650, and it soon became apparent that she was blind. They would have three more children, Elizabeth, Thomas and John.

Between 1656 when he published his first work, Some Gospel Truths Opened (a tract against the Quakers), and his death in 1688, Bunyan published 42 titles. A further two works, including his Last Sermon, were published the following year by George Larkin. In 1692 Southwark comb-maker Charles Doe, who was a friend of Bunyan's later years, brought out, with the collaboration of Bunyan's widow, a collection of the author's works, including 12 previously unpublished titles, mostly sermons. Six years later Doe published The Heavenly Footman and finally in 1765 Relation of My Imprisonment was published, giving a total of 58 published titles.

In 1658 Bunyan's wife died, leaving him with four small children, one of them blind. A year later he married an eighteen-year-old woman named Elizabeth.

The religious tolerance which had allowed Bunyan the freedom to preach became curtailed with the restoration of the monarchy in 1660. The members of the Bedford Meeting were no longer able to meet in St John's church, which they had been sharing with the Anglican congregation. That November, Bunyan was preaching at Lower Samsell, a farm near the village of Westoning, thirteen miles from Bedford, when he was warned that a warrant was out for his arrest. Deciding not to make an escape, he was arrested and brought before the local magistrate Sir Francis Wingate, at Harlington House. The Act of Uniformity, which made it compulsory for Preachers to be ordained by an Anglican bishop and for the revised Book of Common Prayer to be used in church services, was still two years away, and the Act of Conventicles, which made it illegal to hold religious meetings of five or more people outside the Church of England was not passed until 1664. Bunyan was arrested under the Conventicle Act of 1593, which made it an offence to attend a religious gathering other than at the parish church with more than five people outside their family. The offence was punishable by 3 months imprisonment followed by banishment or execution if the person then failed to promise not to re-offend. The Act had been little used, and Bunyan's arrest was probably due in part to concerns that non-conformist religious meetings were being held as a cover for people plotting against the king (although this was not the case with Bunyan's meetings).

The trial of Bunyan took place in January 1661 at the quarter sessions in Bedford, before a group of magistrates under John Kelynge, who would later help to draw up the Act of Uniformity. Bunyan, who had been held in prison since his arrest, was indicted of having "devilishly and perniciousy abstained from coming to church to hear Divine service" and having held "several unlawful meetings and conventicles, to the great disturbance and distraction of the good subjects of this kingdom". He was sentenced to three months imprisonment with transportation to follow if at the end of this time he didn't agree to attend the parish church and desist from preaching.

Two events marred Bunyan's life during the later 1670s. Firstly he became embroiled in a scandal concerning a young woman called Agnes Beaumont. When going to preach in Gamlingay in 1674 he allowed Beaumont, a member of the Bedford Meeting, to ride pillion on his horse, much to the anger of her father, who then died suddenly. His daughter was initially suspected of poisoning him, though the coroner found he had died of natural causes. And then in 1676-7 he underwent a second term of imprisonment, probably for refusing to attend the parish church. This second imprisonment lasted six months.

In prison, Bunyan had a copy of the Bible and of John Foxe's Book of Martyrs, as well as writing materials. He also had at times the company of other Preachers who had been imprisoned. It was in Bedford Gaol that he wrote Grace Abounding and started work on The Pilgrim's Progress, as well as penning several tracts that may have brought him a little money. In 1671, while still in prison, he was chosen as pastor of the Bedford Meeting. By that time there was a mood of increasing religious toleration in the country and in March 1672 the king issued a declaration of indulgence which suspended penal laws against nonconformists. Thousands of nonconformists were released from prison, amongst them Bunyan and five of his fellow inmates of Bedford Gaol. Bunyan was freed in May 1672 and immediately obtained a licence to preach under the declaration of indulgence.

Following his release from gaol in 1672 Bunyan probably did not return to his former occupation of tinker. Instead he devoted his time to writing and preaching. He continued as pastor of the Bedford Meeting and travelled over Bedfordshire and adjoining counties on horseback to preach, becoming known affectionately as "Bishop Bunyan". His preaching also took him to London, where Lord Mayor Sir John Shorter became a friend and presented him with a silver-mounted walking stick. The Pilgrim's Progress was published in 1678 by Nathaniel Ponder and immediately became popular, though probably making more money for its publisher than for its author.

It is the allegory The Pilgrim's Progress, written during Bunyan's twelve-year imprisonment although not published until 1678 six years after his release, that made Bunyan's name as an author with its immediate success. It remains the book for which Bunyan is best remembered. The images Bunyan uses in The Pilgrim's Progress are reflections of images from his own world; the strait gate is a version of the wicket gate at Elstow Abbey church, the Slough of Despond is a reflection of Squitch Fen, a wet and mossy area near his cottage in Harrowden, the Delectable Mountains are an image of the Chiltern Hills surrounding Bedfordshire. Even his characters, like the Evangelist as influenced by John Gifford, are reflections of real people. Further allegorical works were to follow: The Life and Death of Mr. Badman (1680), Pilgrim's Progress Part II, and The Holy War (1682). Grace Abounding to the Chief of Sinners, a spiritual autobiography was published in 1666, when he was still in jail.

In 1688, on his way to London, Bunyan made a detour to Reading, Berkshire, to try and resolve a quarrel between a father and son. Continuing to London to the house of his friend, grocer John Strudwick of Snow Hill in the City of London, he was caught in a storm and fell ill with a fever. He died in Strudwick's house on the morning of 31 August 1688 and was buried in the tomb belonging to Strudwick in Bunhill Fields nonconformist burial ground in London.

Bunyan's estate at his death was worth £42 19s 0d. His widow Elizabeth died in 1691.

Bunyan is best remembered for The Pilgrim's Progress, a book which gained immediate popularity. By 1692, four years after the author's death, publisher Charles Doe estimated that 100,000 copies had been printed in England, as well as editions "in France, Holland, New England and Welch". By 1938, 250 years after Bunyan's death, more than 1,300 editions of the book had been printed.

During the 18th century Bunyan's unpolished style fell out of favour, but his popularity returned with Romanticism, poet Robert Southey writing an appreciative biography in 1830. Bunyan's reputation was further enhanced by the evangelical revival and he became a favourite author of the Victorians. The tercentenary of Bunyan's birth, celebrated in 1928, elicited praise from his former adversary, the Church of England. Although popular interest in Bunyan waned during the second half of the twentieth century, academic interest in the Writer has increased and Oxford University Press brought out a new edition of his works, beginning in 1976. Authors who have been influenced by Bunyan include Nathaniel Hawthorne, Herman Melville, Charles Dickens, Louisa May Alcott and George Bernard Shaw.

In 1862 a recumbent statue was created to adorn Bunyan's grave; it was restored in 1922.

In 1874, a bronze statue of John Bunyan, sculpted by Sir Joseph Edgar Boehm, was erected in Bedford. This stands at the south-western corner of St Peter's Green, facing down Bedford's High Street. The site was chosen by Boehm for its significance as a crossroads. Bunyan is depicted expounding the Bible, to an invisible congregation, with a broken fetter representing his imprisonment by his left foot. There are three scenes from "The Pilgrim's Progress" on the stone plinth: Christian at the wicket gate; his fight with Apollyon; and losing his burden at the foot of the cross of Jesus. The statue was unveiled by Lady Augusta Stanley, wife of the Dean of Westminster, on Wednesday 10 June 1874. In 1876 the Duke of Bedford gave bronze doors by Frederick Thrupp depicting scenes from The Pilgrim's Progress to the John Bunyan Meeting (the former Bedford Meeting which had been renamed in Bunyan's honour, and now houses the John Bunyan Museum).

Bunyan's later years, in spite of another shorter term of imprisonment, were spent in relative comfort as a popular author and preacher, and pastor of the Bedford Meeting. He died aged 59 after falling ill on a journey to London and is buried in Bunhill Fields. The Pilgrim's Progress became one of the most published books in the English language; 1,300 editions having been printed by 1938, 250 years after the author's death.

Bunyan's work, in particular The Pilgrim's Progress, has reached a wider audience through stage productions, film, TV, and radio. An opera by Ralph Vaughan Williams based on The Pilgrim's Progress was first performed at the Royal Opera House in 1951 as part of the Festival of Britain and revived in 2012 by the English National Opera.

John Bunyan had six children, five of whom are known to have married, of which four had children. Moot Hall Museum (in Elstow) has a record of John's descendants, down to the nineteenth century but as of September 2013, no verifiable trace of later descendants has been found.