At the same time as this war was breaking out, the English King, Charles 2nd, was succeeded by King James 2nd. James was a Catholic and introduced laws for religious toleration of non-Anglicans (i.e. Catholics and Presbyterians). However, when James began promoting Catholics up to the higher ranks of the army, Parliament became suspicious that he was trying to make England an officially Catholic country again. To complicate matters, James' daughter, Mary, married William of Orange and thus William became heir to the throne.

In 1687, James made his brother-in-law his viceroy in Ireland. The viceroy strengthened the Irish army in case James needed it. Because James was a Catholic, it was easy to find recruits in Ireland. However, when the viceroy tried to garrison some of the Catholic troops in Derry in 1688, the Protestant citizens did not want them to enter. Nobody was brave enough to go and tell the troops they were not welcome, however, and eventually it was the young apprentice boys of Derry who shut the city gates as the troops tried to enter. This was repeated in Enniskillen, in Co Fermanagh. It is these events that today's Apprentice Boys commemorate.

Things changed for the worse in 1688 when James had another son. However, while James regarded this Catholic boy as his heir, Parliament regarded Protestant William as heir. Scared that James would take action to prevent William becoming King, Parliament invited William over to take over the monarchy there and then, and William duly arrived in November 1688 with his troops and marched to London. James fled to France and William and Mary were made King and Queen in 1689. This coronation is called the 'Glorious Revolution'. The Protestants in Ireland joined the revolution and declared their support for William.

In March 1689, James landed in Ireland at Dublin to start his fight-back, because he knew he would get strong Catholic support there. Many Protestants, in support of William, took up arms and attacked James' new army. However James was stronger than the natives and drove them back and sieged them in the cities of Derry and Enniskillen, with the aim of crushing all Williamite support in Ireland. James placed a boom across the Foyle River so Derry was without food supplies for 105 days. The situation got so desperate that astronomical prices were being paid in the city for things like a single rat. The siege of Derry is another of the famous events of Irish history. The siege was finally lifted when a Williamite ship, the Mountjoy, arrived and smashed through the boom on 28 July 1689 and James fled. James’ soldiers who had been sieging Enniskillen were intercepted and defeated at Newtownbutler, Co Fermanagh. In August 1689, William’s armies landed at, and took, the town of Carrickfergus in Co Antrim.

In March 1690, 4000 Grand Alliance troops (Danes, in fact) arrived at Belfast to aid William, because they wanted William to get back to leading the war in Europe. At the same time, Louis 16th of France sent troops to aid James. He wanted to prolong the war in Ireland, so that William's attention would be diverted away from France for longer. In June 1690, William himself arrived at Carrickfergus and marched south. James marched north from Dublin and the two armies met at the River Boyne, in Co Meath on 1 July, 1690. The ensuing battle, known as the Battle of the Boyne, is arguably the most famous event in Irish history, due to its symbolic Catholic/Protestant confrontation.

In the event, William won the battle losing 400 men to James' 1,300. James immediately left for Dublin and subsequently fled to France. William's victory was celebrated right across Europe as it represented a defeat by the Grand Alliance over France. James' viceroy remained and led the remains of James' army to Limerick and Athlone. He managed to inflict several defeats on William's army, and William failed to take Limerick despite sieging it. William returned to England leaving his general Ginkel in charge. Ginkel offered the Jacobites (supporters of James) a peace settlement, but they refused and decided to fight on under the leadership of the Marquis St Ruth. On 12 July, 1691 the two armies met at Aughrim, near Athlone. Ginkel decided to attack despite being in an inferior strategic position. However, he won and St Ruth was killed and the Jacobites retreated in disarray to Limerick. On 26 September 1691, the Jacobites finally surrendered and a peace treaty was signed in October 1691. This was the Treaty of Limerick which permitted Catholics to retain the right to practice their religion, but forfeit their land. Most of the Jacobite soldiers were allowed free passage to go to France to fight for Louis, and were known as the 'Wild Geese'.