Henry was the son of Edward Willoughby (d 1541) and his wife Anne, daughter of Sir William Filliol of Woodlands, Dorset. Anne Filliol was the sole heiress of Woodlands, since her sister Katherine, wife of Edward Seymour, Protector Somerset, was cut out of her father's will. Henry's grandfather was Sir Henry Willoughby (1451-1528) of Wollaton and Middleton.
Henry inherited the Woodlands estate when his father died in 1541, and the Wollaton and Middleton estates from his uncle Sir John Willoughby in January 1548/9. He was only able to enjoy this inheritance for a few months, as he died in August 1549 while fighting in Kett's Rebellion, leaving three young children.
Henry married Anne Grey, daughter of Thomas, 2nd Marquess of Dorset, and had:
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