Edmund Mortimer, 5th Earl of March, was born at New Forest, Westmeath, one of his family's Irish estates, on 6 November 1391, the son of Roger Mortimer, 4th Earl of March, and Eleanor Holland. He had a younger brother, Roger (1393 – c. 1413), and two sisters: Anne, who married Richard, Earl of Cambridge, younger son of the Duke of York (executed 1415); and Eleanor, who married Sir Edward de Courtenay (d. 1418), and had no issue.
Edmund Mortimer's mother was the daughter of Thomas Holland, 2nd Earl of Kent, and Alice FitzAlan. Thomas Holland's mother, Joan of Kent, a granddaughter of Edward I, was the mother of Richard II by her second marriage; Alice Fitzalan was the daughter of Richard FitzAlan, 10th Earl of Arundel, and his second wife, Eleanor, daughter of Henry, 3rd Earl of Lancaster, grandson of King Henry III.
Edmund Mortimer was thus a descendant of Henry III and Edward I and a half-great-nephew of Richard II through his mother, and more importantly a descendant of King Edward III through his paternal grandmother Philippa of Clarence, only child of King Edward III's second surviving son, Lionel of Antwerp, Duke of Clarence. Because King Richard II had no issue, Edmund's father, Roger Mortimer, 4th Earl of March, was heir presumptive during his lifetime, and at his death in Ireland on 20 July 1398 his claim to the throne passed to his eldest son, Edmund. Thus in terms of male primogeniture Edmund was heir to the throne over and above the house of Lancaster, the children of Edward III's third son John of Gaunt, Duke of Lancaster.
However, on 30 September 1399, when Edmund Mortimer was not yet eight years of age, his fortunes changed entirely. Richard II was deposed by Henry Bolingbroke, the new Duke of Lancaster, who became King Henry IV and had his own son, the future King Henry V, recognized as heir apparent at his first Parliament. The King put the young Edmund and his brother Roger in the custody of Sir Hugh Waterton at Windsor and Berkhampstead castles, but they were treated honourably, and for part of the time brought up with the King's own children, John and Philippa.