Boyle was born at Lismore Castle, in County Waterford, Ireland, the seventh son and fourteenth child of The 1st Earl of Cork (the Great Earl of Cork) and Catherine Fenton. Lord Cork, then known simply as Richard Boyle, had arrived in Dublin from England in 1588 during the Tudor plantations of Ireland and obtained an appointment as a deputy escheator. He had amassed enormous wealth and landholdings by the time Robert was born and had been created Earl of Cork in October 1620. Catherine Fenton, Countess of Cork, was the daughter of Sir Geoffrey Fenton, the former Secretary of State for Ireland, who was born in Dublin in 1539, and Alice Weston, the daughter of Robert Weston, who was born in Lismore in 1541.
As a child, Boyle was raised by a wet nurse, as were his elder brothers. Boyle received private tutoring in Latin, Greek, and French and when he was eight years old, following the death of his mother, he, and his brother Francis, were sent to Eton College in England. His father's friend, Sir Henry Wotton, was then the provost of the college.
During this time, his father hired a private tutor, Robert Carew, who had knowledge of Irish, to act as private tutor to his sons in Eton. However, "only Mr. Robert sometimes desires it [Irish] and is a little entered in it", but despite the "many reasons" given by Carew to turn their attentions to it, "they practice the French and Latin but they affect not the Irish". After spending over three years at Eton, Robert travelled abroad with a French tutor. They visited Italy in 1641 and remained in Florence during the winter of that year studying the "paradoxes of the great star-gazer", the elderly Galileo Galilei.