As a young girl, she was at court as a lady in waiting first to Elizabeth of York and then to Catalina of Aragon. Her brother, Thomas Howard, 3rd Duke of Norfolk, was the most powerful nobleman in England and it is generally accepted that, with the exception of his wife he controlled the rest of his family, including his sister’s husband and children.

It was while she was at court, that she wed Thomas Boleyn, an ambitious young courtier, sometime before 1500, probably in 1498. According to Thomas, his wife was pregnant many times in the next few years but only five children are thought to have survived birth and only three into adulthood. Elizabeth Howard is most famous for having been the mother of Anne Boleyn, who became the second wife of Henry VIII of England. As such, she was also the maternal grandmother of Queen Elizabeth I. It once was believed that Elizabeth Howard died young and her children were raised by a stepmother, but documentary evidence has since disproved this.

Elizabeth Boleyn must have been a highly attractive woman. Rumours circulated when Henry was involved with Anne Boleyn that Elizabeth had once been his mistress, with the suggestion even being made that Anne Boleyn might be the daughter of Henry VIII. However, despite recent attempts by one or two historians to rehabilitate this myth, it was denied by Henry and never mentioned in the dispensation he sought in order to make his union with Anne lawful. Most historians believe it is likely that this rumour began by confusing Elizabeth with Henry's more famous mistress Elizabeth Blount, or from the growing unpopularity of the Boleyn family after 1527.

In 1519, Elizabeth's daughters, Mary and Anne, were living in the French royal court as Ladies-in-waiting to the Queen Claude. According to the papal nuncio in France fifteen years later, the French King Francois I had referred to Mary as, "my English mare"; and later in his life described her as "a great whore, the most infamous of all".

In the words of historian M.L. Bruce, both Thomas and Elizabeth "developed feelings of dislike" for their daughter, Mary. In later years, Mary's romantic involvements would only further strain this relationship. Around 1520, the Boleyns managed to arrange Mary's marriage to Sir William Carey, a respected and popular man at court. It was sometime after the wedding that Mary became mistress to Henry VIII (the exact dates as to when the affair started and ended are unknown). It has long been rumoured that one or both of Mary Boleyn's children were fathered by Henry and not Carey. Some historians now question whether Henry Carey was fathered by the King.

In contrast to Mary, Elizabeth's other daughter, Anne, is thought to have had a close relationship with her mother. Elizabeth had been in charge of Anne's early education and she had taught her music and religion, as well as embroidery, reading and writing. In 1525, Henry VIII fell in love with Anne, and Elizabeth became her protective chaperone. She accompanied Anne to Court, since Anne was attempting to avoid a sexual relationship with the King. Elizabeth travelled with Anne to view York Place after the fall of the Boleyn family's great political opponent, Cardinal Thomas Wolsey — an intrigue which had given Anne her first real taste of political power. She was crowned queen four years later.

Elizabeth remained in her daughter's household throughout her time as queen consort. Tradition has it that Anne's daughter, Elizabeth, was named after her maternal grandmother. However, it is more likely that she was named after Henry's mother, Elizabeth of York, although we cannot rule out the possibility that she was named after both grandmothers.

Elizabeth Boleyn sided with the rest of the family when her eldest daughter, Mary, was banished in 1535 for eloping with a commoner, William Stafford. Mary had initially expected her sister's support (Anne had been Mary's only confidante within the Boleyn family since 1529). But Anne was furious at the breach of etiquette and refused to receive her.

Only a year later, the family was overtaken by a greater scandal. Anne and George, were executed on charges of treason, adultery and incest. The King wanted to marry Jane Seymour. Academic historians agree that Anne was innocent and faithful to her husband. Nonetheless, the judges obeyed the King, condemning Anne, George Boleyn and four others to death. Elizabeth's husband, Thomas Boleyn and brother Thomas Howard, 3rd Duke of Norfolk, were no help to the condemned. The accused men were beheaded by the axe on 17 May 1536 and Henry's marriage to Anne was annulled, on the grounds of his previous relationship with her sister. This made Elizabeth's granddaughter, then heir to the throne, a bastard of doubtful paternity.

Following the annihilation of the family's ambitions, Elizabeth retired to the countryside. She died only two years after her children and her husband died the following year.