Because of James' conversion to the Catholic faith, three attempts were made in Parliament to exclude him from the succession to the throne; none of these was successful. At the death of his brother Charles II, February 6, 1685, James succeeded as king. He was crowned privately according to the rites of the Catholic Church, April 22, 1685, at Whitehall Palace, and publicly according to the rites of the Church of England, April 23, 1685, at Westminster Abbey.

Always an advocate of liberty of consicence, James published a Declaration of Toleration for Scotland, February 12, 1686. He issued an even more liberal Declaration of Indulgence for England, April 4, 1687; this he re-issued April 27, 1688 with an order that it be read in all churches. Seven bishops petitioned against this order.

On June 30, 1688, five English peers and two commoners sent an invitation to James' son-in-law and nephew the Prince of Orange to invade England by force. On September 28, James published a proclamation against the forthcoming invasion. William Henry, Prince of Orange realised the power of the press and was urged by his advisors to ensure that he took a printing press with him on his expedition. This sheet was printed in advance of his expedition to strike the first blow in the propaganda battle. The Prince of Orange issued several declarations, September 30, October 10, and October 24, in each of which he stated his intention to restore the former state of religious oppression.

On November 5, the Prince of Orange landed at Brixham with an army of 15,000. On December 11, James withdrew from London with the intention of retiring temporarily to France. This first effort was thwarted, but a second on December 23 was successful. A Convention of the Lords Spiritual and Temporal, and Commons, thereupon assembled at Westminster, and on February 13, 1689, published a declaration that James had abdicated the government. On April 11, 1689, a Convention of the Scottish Estates made a similar declaration.

James retired to the Château of St. Germain-en-Laye where he continued to be recognised as king by the Most Christian King until the Treaty of Ryswick in 1697; on June 8, 1697, James published a protest against this treaty.

James died September 16, 1701, at the Château of St. Germain-en-Laye, when he was succeeded in all his British rights by his son James. His body was lain (in a coffin, but not buried) in the Chapel of Saint Edmund in the Church of the English Benedictines in the Rue St. Jacques, Paris. His brain was sent to the Scots College in Paris, his heart to the Convent of the Visitandine Nuns at Chaillot, and his bowels divided between the English Church of St. Omer and the parish church of St. Germain-en-Laye. James' body remained in the Church of the English Benedictines, waiting translation to Westminster Abbey, until the French Revolution when it were desecrated by the mob and lost. Lost also during the Revolution were his remains at the Scots College, the Visitandine Convent of Chaillot, and the English Church of St. Omer. The praecordia which had been placed in the parish church of St. Germain-en-Laye, however, were rediscovered in 1824 and remain there to this day.