For his behaviour he was fined, publicly whipped, pilloried and finally imprisoned, receiving increasingly harsh punishment because he would not stop attacking the authority of the bishops. As David HUME wrote later, ‘It was found difficult to break the spirits of men, who placed both their honour and their conscience in suffering’ (Hume 1778, vol. 5: 244). Lilburne remained in prison until he was finally liberated by the Long Parliament in 1640 after a speech on his behalf by Cromwell. Lilburne then tried to lead a settled life by becoming a brewer and getting married, but his religious and political principles would not allow him to lead a quiet life.

When the English Civil War broke out in 1642, Lilburne was commissioned as a captain in the parliamentary army. He was a successful and popular officer, and reached the rank of lieutenant-colonel. In 1644 he resigned from the army rather than subscribe to the Solemn League and Covenant with Scotland, which required the Church of England to be reformed along Presbyterian lines. His opposition to the oath seems to have been principled: he objected to being forced to swear any kind of religious oath, regardless of whether he had sympathies with its doctrines or not.

Thereafter Lilburne became the most famous - or infamous - leader of the Levellers, a group of political agitators opposing Cromwell and seeking extension of the franchise and other democratic rights. Lilburne's strong, frequently dominating personality made it at times difficult to separate the Levellers as a movement from Lilburne himself. He was vocal, tireless, public and aggressive. He issued a stream of pamphlets and speeches denouncing, among other things, parliament, parts of the army, and Cromwell. None of those groups or persons would meet Leveller demands in full, and Lilburne would not let them deviate without public excoriation. He was again arrested for his agitation, and spent most of August 1645 to August 1647 in prison. He was not deterred from his activities, and on 1 May 1649, while imprisoned yet again, he issued his third Agreement of the People, by which means he was able to muster support from both the army and in London. On 2 May some of the troops under the command of Ireton and Cromwell refused orders; this led to the mutiny of further troops, until by 14 May some twelve hundred men were refusing orders, demanding instead the release of Lilburne and the other Levellers. In response, on 14 May 1649 Cromwell and a contingent of the loyal troops surprised and crushed the Levellers army near Burford, Oxfordshire, effectively putting an end to them as an organized political movement.

Despite the defeat of the Leveller movement, Lilburne maintained his popularity among Londoners, symbolized by the thousands of sympathizers wearing the Levellers' characteristic sea-green ribbons on hats and clothing. Lilburne was tried for treason in 1649 and again in 1653, both times defending himself and both times arguing to the jury, in defiance of the explicit instructions of the judge, that they were empowered to judge not only the facts but also the law. The jury acquitted him on both occasions. The second acquittal led to a large popular demonstration in support of Lilburne, an action that sufficiently worried the government that Cromwell decided to keep Lilburne in prison, the acquittal notwithstanding, until 1655. In that year Lilburne converted to the Quaker faith and apparently gave up his more vocal, confrontational ways for the last two years of his life. In 1657, his health was failing, he was granted a parole to visit his wife, Elizabeth, in Eltham, where he then died aged forty-three.

Although he was not a systematic thinker, Lilburne's agitations nevertheless formed a coherent philosophy of individualism. Men are equal insofar as each is essentially an individual, and under natural law they have natural rights that precede and trump manmade legal rights. Each person is also equal insofar as he possesses reason, which, when exercised properly, will apprehend not only the natural law and its entailed individual rights, but also their self-evident authority. One of the basic rights each man has by nature is sovereignty over his conscience, which includes the right to practice religion as his conscience dictates and to speak, write and petition freely. No government is legitimate that cannot be justified as a social contract or compact entered into by the voluntary consent of the governed.

Lilburne was thus a radical individualist. Popularly dubbed ‘Free-Born John’, he believed that he, like every other Englishman, was born free, that he was a citizen of England rather than a subject, and that it was he and other individuals that gave rise to the state, not the reverse. His advocacy of freedom of religion was absolute, even in the face of arguments from Cromwell, Ireton and others during the Putney debates of 1647 that such freedom would create, in Ireton's words, ‘utter confusion’ in the realm. Ireton was indeed startled by ‘that wild and vast notion’ of freedom advocated by Lilburne and the other Levellers, and he shuddered ‘at the boundless and endless consequences of it’. But Lilburne would not be dissuaded.

Lilburne derived several specific political policies from his individualist premises. These included the right to be free of arbitrary seizures, to a trial by jury, and to face one's accusers in open court. He also called for the extension of the franchise to all the freeborn men of England. Although he developed no economic theory per se, he nevertheless advocated several specific policies that we today would recognize as having far-reaching economic consequences: free trade, private property and an abolition of economic privileges like state-enforced monopolies. Lilburne denounced, for example, the Levant Company's chartered monopoly of trade with the Middle East, arguing that the right to trade with whomever one wished was one of mankind's natural rights; William Walwyn later expanded this argument in his For a Free Trade (1652). Moreover, Lilburne supported private property as another of mankind's natural rights, and in so doing he carefully and emphatically distanced himself from other groups - particularly the Diggers, under the leadership of Gerrard Winstanley - who were calling for either common ownership or a redistribution of property holdings on a more equal basis. Lilburne was not a leveller in that sense: he advocated levelling all men before the law, but not in holdings or private property. Thus he was one of the earliest advocates of what would come to be recognized as British classical liberalism, supporting free markets almost 150 years before Adam Smith and private property some fifty years before John Locke.

Lilburne was not a scholar, and he wrote no extended treatises of philosophy or history; the life of a publicist and activist suited his temperament more than did the contemplative life of a philosopher. But he had a vision of individual freedom for which he was willing to die. Subsequent generations of liberals would not only find this inspirational but would develop Lilburne's views into more comprehensive moral, political and economic systems. Hume concluded that Lilburne was ‘the most turbulent, but most upright and courageous of human kind’ (Hume 1778, vol. 6: 39).