On 14 November 1501, Elizabeth of York's 15-year-old son Arthur married Catherine of Aragon, daughter of King Ferdinand II of Aragon and Queen Isabella I of Castile. The pair were sent to Ludlow Castle, the traditional residence of the Prince of Wales. Arthur died in April 1502. The news of Arthur's death caused Henry VII to break down in grief, as much in fear for his dynasty as in mourning for his son. Elizabeth comforted him, telling him that he was the only child of his mother but had survived to become king, that God had left him with a son and two daughters, and that they were both young enough to have more children.

Her marriage seems to have been successful, though her eldest son Arthur, Prince of Wales, died at age 15 in 1502, and three other children died young. She seems to have played little part in politics. Her surviving children became a king of England and queens of France and Scotland; it is through the Scottish Stuart dynasty that her many modern royal descendants trace their descent from her.

The Tower of London was abandoned as a royal residence, evidenced by the lack of records of it being used by the royal family or Henry Tudor after 1503. All Future births in the reign of Elizabeth's son, Henry VIII, took place in palaces.

In 2012, the Vaux Passional, an illuminated manuscript that was once the property of Henry VII, was rediscovered in the National Library of Wales. It depicts the aftermath of Elizabeth's death vividly. Henry VII is shown receiving the book containing the manuscript in mourning robes with a doleful expression on his face. In the background, behind their father, are the late queen's daughters, Mary and Margaret, in black veils. An 11-year-old King Henry VIII's red head is shown weeping into the sheets of his mother's empty bed.

Henry VII entertained thoughts of remarriage to renew the alliance with Spain — Joanna, Dowager Queen of Naples (niece of Ferdinand II of Aragon), Joanna, Queen of Castile (daughter of Ferdinand and Isabella), and Margaret, Dowager Duchess of Savoy (sister-in-law of Joanna of Castile), were all considered — but he died a widower in 1509. Annually on her death day, he decreed a requiem mass be sung, the bells be tolled, and 100 candles be lit in her honour.

Elizabeth of York was born at the Palace of Westminster as the eldest child of King Edward IV and his wife Elizabeth Woodville. Her christening was celebrated at Westminster Abbey, sponsored by her grandmothers Jacquetta of Luxembourg, Duchess of Bedford, and Cecily Neville, Duchess of York. Her third sponsor was her cousin Richard Neville, 16th Earl of Warwick.