He was born in 1634 in Castletown Kildrought, now Celbridge, County Kildare in the Kingdom of Ireland. He was the youngest son of Sir John Dongan, Baronet, Member of the Irish Parliament. As Catholics, his family faced persecution after the overthrow of Charles I and fled to France. While in France, he served in an Irish regiment with Turenne. He continued to stay in France after the Restoration and achieved the rank of colonel in 1674.

After the Treaty of Nijmegen ended the French-Dutch War in 1678, Dongan returned to England in obedience to the order that recalled all English subjects fighting in service to France. James, Duke of York, who had served as a fellow officer of Dongan's in French army, arranged to have him granted a pension and high-ranking commission in the army and designated for service in Flanders. That same year, he was appointed Lieutenant-Governor of Tangiers.

In 1682, James I of England, who had become the Lord Proprietor of the Province of New York after it was acquired from the Dutch, appointed Dongan as provincial governor and granted him an estate on Staten Island.

At the time of his appointment, the province was bankrupt and in a state of rebellion caused by the mismanagement of the previous governor. Dongan was able to restore order and stability through tactful means. On October 14, 1683, he convened the first-ever representative assembly in New York history, which convened at Fort James.

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