Egbert was the son of King Erconbert of Kent and his wife, Sexburga the daughter of King Anna of East Anglia. Erconbert had only inherited the throne because his elder brother, Ermenred, had predeceased their father. Therefore, although it seemed natural for Egbert to succeed to the throne upon his own father's death in AD 664, it could be argued that Ermenred's young sons - being now old enough to rule themselves, had a prior claim. Perhaps there was some support for them, for Egbert certainly appears to have felt that his position was not as secure as it might be. His cousins, Aethelred and Aethelbert, are said to have been of a devout disposition and actually posed him little threat. But, around AD 666, one of Egbert's advisors, named Thunnor, persuaded him that the princes must die. The story goes that Egbert never actually plotted their murder himself, but Thunnor soon took matters into his own hands.

Thunnor murdered the two lads at the King's Palace in Eastry and secretly buried their bodies in a shallow grave beneath the great hall. However, when they were missed, a holy light appeared above their sepulchre and revealed their fate. King Egbert was apparently filled with horror and confessed to his previous hopes that such a thing such occur. He was thus obliged to pay weregild (or 'the price of blood') in expiation for his crime and gave the Isle of Thanet to the princes' sister, St. Aebbe. She founded the monastery of Minster-in-Thanet there in their honour, whilst the Royal bodies were reburied with great honour in Wakering Church in Essex (their relics were later removed to Ramsey Abbey)

Perhaps Egbert got religion after this, for, in AD 669, he also founded the monastery within the old Roman fort at Reculver for his priest, Bassa; and Chertsey Abbey, which shows that he ruled Surrey for a time, though he appears to have been pushed out by Wulfhere of Mercia in that same year. Upon his death in AD 673, he was succeeded by his brother, Hlothhere.